Transformers never had a unified continuity. From "go" the Marvel comics and Sunbow cartoon were irreconcilable....they really were trying to be Aligned before Aligned was a thing.
Trying to synthesize a "unified" continuity is nothing new earlier. Beast Wars picked bits from Marvel and Sunbow G1 freely to craft its backstory, and some of the earliest fan discussions online were about people arguing preferences between Marvel and Sunbow, with a lot of energy dedicated to people posting their preferences as to what they preferred to take from each for their personal canon.
The personal canon threads here and elsewhere are testaments to this, a proud tradition of Transformers fans explaining what continuities they preferred and what they took from everything else to craft their own head canons.
This only grew as the franchise eventually expanded beyond just the broad "G1 to Beast Machines" continuity family with RiD, followed by Armada and the rest of the UT. Toss in the Movie and Animated... and suddenly it wasn't just different aspects of G1, there was a whole multiverse of Transformers stories, character concepts, etc... that fans pulled from.
And it wasn't just fans. As stated, the Beast Wars writers drew from both Sunbow and Marvel G1. Beast Machines used a plot point from G1 as a central story element. RiD, the UT, the live action movies, Animated.... they all referenced each other, taking elements from past incarnations, working them with new ideas to flesh out new continuities.
In this sense nothing Aligned did was bad, or even offensive. It was doing what fans and other creators had been doing for years, launching a new Transformers continuity that pulled at plots and ideas from past stories as part of its own world building and character concepts.
The objectionable part of Aligned was trying to be The Final Word And Unified Version From Now On.
For a franchise that didn't even have a unified continuity even when there was only one continuity family, much less multiple new continuities since, it was awfully arrogant. And fundamentally unworkable.
These past discrepancies and continuities happened for reasons.
Be it separate creatives on separate projects who wanted to do their own thing, market forces forcing a reset (the first continuity reboots happening because Beast Machines bombed and a massive rework was needed), or both in tandem.
Nothing was going to change these realities once Aligned was launched. And indeed, that showed early, with the WfC game, the comic adaptation of it, and the book sold as a tie in all presented different versions of events, and even character names. Not to mention Prime's writing staff not wanting to be beholden to Hasbro's mandates for story and Rescue Bots being forced into Aligned against Hasbro's wishes, and IDW just refusing to play along...
Hasbro tried (we talked about how they shoved Aligned and IDW references into the sub scripts for the subtitled releases of the Headmasters, Masterforce, and Victory) but ultimately this didn't work either. Market forces popped up as Prime's toyline sales weren't great, the Hub's viewership was down, and Archer and Alvarez were shown the door and suddenly the continuity that was going to be The One Way Things Are Forever ended up as just another continuity reset in a long line of them.
All the while fans and creatives are still doing what they've always done. Drawing from past continuities and mixing those ideas with new ideas to create new head canons or continuities.
tl;dr the desire to make the disparate past all work together isn't unique to Aligned, it's something that's always been there with this franchise. Aligned was just the one that thought it was special.