When Seasons 2 and 3 of the American BW cartoon were held back from being dubbed in Japan until later (since there weren't enough episodes in Season 2 alone to run for a full year in Japan), Beast Wars Second and Neo were created to fill in the gap during the wait. But, both were going off the world-building done only by the first season of Beast Wars, completely unaware of all the retcons that Seasons 2 and 3 would come to later make. In Season 1, Megatron was presented as the sole ruler of the Predacons, who likewise were said to be a faction of conquerors bent of ruling the galaxy. Thus, BWII and Neo featured Galvatron and Magmatron as powerful emperors with spacefaring starships and vast resources at their disposal.
No one making those shows knew anything about Beast Wars season 2 having revealed the Predacons to instead be second-class citizens under the Maximal government, Megatron to instead be viewed as lowly criminal with delusions of grandeur by his own people, and the Predacons to actually be ruled by the Predacon Alliance during a peacetime known as the Pax Cybertronia. All of which flew right in the face of how the Predacons were depicted in both BWII and Neo. All because Season 2 and 3 Beast Wars had changed so much about Megatron and the Predacons from how they were presented in Season 1.
And then there's the whole thing with Optimus, or "Convoy". The first toy catalog for BWII was still going off those early impressions that Takara had had about Beast Wars Optimus and Megatron, and so depicted them as the immediate predecessors to Lio Convoy and Galvatron, with the catalog saying that Convoy and Megatron were immediately succeeded by both of them when Convoy and Megatron left Cybertron to go fight in the Beast Wars. This was further illustrated in the BWII manga, in which Convoy was shown to be a high-ranking member of a military council on Cybertron. A short bio written for him even described him as "A fierce fighter who has fought against the Destron army for thousands of years." He then guest-starred in the BWII movie, in which he was revered as a "legendary Supreme Commander", complete with his own Matrix! That's a far cry from the lowly science ship captain Optimus Primal actually was in the English version, sounding an awful lot more like Optimus Prime instead.
When Seasons 2 and 3 finally reached Japan in 1999, everything Takara thought they understood about Beast Wars was turned on its head by all the new reveals mentioned above. The Japanese dub of Metals leaned into the English version's way of thinking, making it clear that BW Convoy and Megatron were NOT G1 Convoy and Megatron after all, Megatron was not the ruler of all Predacons but just his own small gang of criminals, and the Predacons themselves were not galactic conquerors but merely disgruntled citizens ruled by their own government subservient to that of the Maximals. In other words, BWII and Neo were suddenly very incompatible with the show they were originally created to be spinoffs of.
When Car Robots was made, it seemed like Takara tried to backtrack things a bit in order to make things align a little better with what all had been said and done in Metals, in an attempt smooth things over between it and BWII and Neo. Instead of continuing to call the Predacons the same Japanese name as the Decepticons, "Destron" was changed to "Destronger", evoking the change from "Decepticon" to "Predacon" in the western world. Stasis pods and protoforms (which had both been absent in BWII and Neo) were brought back in, complete with an ancient ship based on the Axalon containing them. And elements like the Energon Matrix and Vector Sigma being the Transformers god were worked in to better tie things together with BWII and Neo.
BUT, all that was still done without any awareness of what was going on with Beast Machines, which itself wasn't brought over to Japan until 2004! In Beast Machines, Vector Sigma was not the public figure it was in Beast Wars Neo, it was ancient long-forgotten legend that had been hidden away deep down far below the surface of Cybertron. And it wasn't even remembered by its original name, but instead by the name of its evolved form, "the Oracle". There was no way Beast Wars Neo could take place before Beast Machines if Vector Sigma was supposed to be this long lost legend in BM, when it was instead a very well-known thing placed high up in a very open-to-the-public city tower in Neo. To make matters worse, BM ended with Cybertron being reformatted into a technorganic state when both Neo and Car Robots had presented the planet in its traditional metallic state, both shows having been unaware of the reformatting that was going to happen at the end of BM.
So, what Takara was left with was a great big mess of their own making to clean up. They had made two shows spun off from the first season of one show whose second and third seasons would later upend everything Takara was led to believe about this shared universe from what was first told about it in the first season. So when they tried use Car Robots to bandage some the discrepancies, Beast Machines made the Takara shows even more incompatible. So what was Takara left to do? They stuck to their guns by adhering to the truths established by the American cartoons, and then cordoned off and relocated the Japanese shows to instead take place somewhere else far off and away from the American cartoons that they no longer fit in with.
And they did so by also leaning into what was true in those Japanese shows. In BWII, the planet Gaia is shown to be a post-apocalyptic Earth, stated in Episode 36 to have long been abandoned by humanity for tens of millennia. Even before Metals was dubbed in Japanese, this already contradicted the BW episode "Dark Designs", in which it was stated that the Great War between the Autobots and Decepticons was "three centuries ago". That discrepancy automatically pushed BWII to come way later than intended. While one could make the argument that the Great War could have continued for many millennia into the future, Beast Wars Neo would later state that the "Great War" (referred to by that name spoken in English, no less) officially ended with the destruction of Unicron in the 21st century. Not to mention the fact that Beast Wars Neo's first episode opens with full Maximal and Predacon armies openly engaged in all-out war, which is completely at odds with the peace accord of the Pax Cybertronia. Combining all that information, Beast Wars and Beast Machines had to take place in the 24th century, while BWII and Neo had to instead come eons later.
But then, how exactly would that fit with technorganic reformatting at the end of Beast Machines? Well, that would eventually be patched up by a Legends pack-in comic that showed the reformatting undone eons later when Vector Sigma sensed the looming return of Unicron, with the planet being re-mechanized to better defend itself against Unicron's coming threat, all in foreshadowing the events of Neo. So the planet stayed technorganic for many thousands of years until the danger posed by Unicron forced Vector Sigma to change it back in better preparation for the cosmic devil's return.
This relocation of BWII and Neo also kind of fits with other little details in those shows. The pre-beast forms on the cast of BWII always looked weird and alien, almost organic-like even, which matches up with the technorganic designs of Beast Machines. The BWII cast could scan beast modes with built-in DNA scanners, when the cast of Beast Wars had to use external devices to do that. Beast Machines introduced the concept of DNA scanners being built into Cybertronians as something brand new, with BWII showing them as something ordinary now suddenly making sense as a distant continuation of that. Neo would even go as far as to say that organic beast modes are commonplace on Cybertron, when flashbacks in Beast Machines show that to not be the case. Neo coming long after BM suddenly makes that statement line up very well with BM's technorganic reformatting. Neo even further showed Big Convoy to have special abilities attuned to organic nature, coincidentally not unlike those displayed by the technorganic Maximals (Botanica especially) in BM.
And what about all those other things from before that treated BW Convoy and Megatron as if they were G1 Convoy and Megatron? Well, the Japanese toy bios are now their own little micro-continuity (much like the English toy bios that did the same thing), so too is the toy catalog, the BWII manga was always its own separate continuity from the cartoon, and the BWII movie revering BW Convoy as a legendary hero suddenly now jibes very well with his heroic sacrifice at the end of Beast Machines, as he was the last living good guy on Cybertron and gave his life to literally save every life on the planet. That's certainly a legendary feat of accomplishment. And interestingly, the cast of Beast Wars Neo would also revere Lio Convoy as a "legendary warrior" when Big Convoy and his team first meet him in that series. Heck, Big Convoy himself would even be treated as a "legendary warrior" in his own series, as early as the first episode even!
Essentially, being "legendary" in Japanese Transformers fiction isn't all that special. It's just something typical of long-running children's action series in Japan whenever the current cast of one series gets to meet a member of the previous series's good guy cast and treats them like they're so cool (like in Super Sentai team-ups or Kamen Rider team-ups).
I think that's everything.