Ew, The Game Theorists. Don't particularly care for the jittery video style that seems focused on entertaining short attention spans and capitalizing on clickbait than being good discussion. For this video, they chose the one thing that was easiest to prove and least breaking of the lore. But...I think the act of bringing up the shift in lore is good. So, thank you Shadewing. There's a lot that hasn't been discussed here about Sonic Frontiers and the greater lore implications. I guess it's up to the mods on whether these should be in spoilers since I'm not sure if we're far enough from the release of Frontiers.
I think the first thing is that Sega hired a team to work on consolidating the lore. This include writer Ian Flynn and current Sonic social media manager Katie Chrzanowski. As a 30+ year franchise with multiple writers that's often filtered through translations, there's obvious holes in the lore. Adding to that, it could be argued that the American and Japanese game lore are different canon. That said, there's been efforts to bring them closer.
On the actual lore, I'll start with Sonic Unleashed. Frontiers states that the Chaos Emeralds come from outer space and were brought to earth. Unleashed states that the Chaos Emeralds were in the Gaia Temples and are intrinsic to the battles between Light Gaia and Dark Gaia and the planet's rebirth cycle. This feels like a contradiction, though it could be a timing issue with the Ancients arriving before the Gaia Temples were built. Sonic lore tends to deliberately not use exact time measurements.