Even this early on in the series you can see Primal beginning to deteriorate. Hes constantly losing his monkeyshit and the loss of Cybertron and the Beast Wars is weighing heavily on him. Its no wonder he becomes an extremist.
Rattrap too is deteriorating. He was always cocksure(if pessimistic) and first to grab a gun in a fight. Now hes crippled, helpless, stripped of weapons and desperate - its no wonder her acts the way he does in Weak Component.
The only person who seems incongruent is Megatrons sudden organic hate. But after being torn from the ship in transwarp space, it never states how long hes been gone - it must have been a very long time for him to set his plan in action. What happened to him? How did he do it? Now theres a prequel Id live to see
I agree that Megs’s personality is incongruent, but remember, from his perspective, BILLIONS of years have gone by cus of where in the time stream he got dropped off on Cybertron, or wherever it was he ended up. Who knows what kind of nuttery he encountered in those years. In my personal headcanon (and I feel like this may have influenced IDW Meg’s characterization too) post-BW/pre-BM Megs probably witnessed countless skirmishes between Autobots and Decepticons and later Maximals and Predacons and probably came to the conclusion that the reason his side always lost was because of Earth and it’s influence on the outcomes of all battles in favor of his enemies. Earth culture and presence also probably intermingled with Cybertronian society after the Great War (kind of like post-IDW 2005) to kind of cement and celebrate the cooperative history of Earth and the Autobots bringing them victory over the Decepticons, which lead to the Preds being slaves as Megs sees it. And so, much like what he started in that valley on prehistoric Earth, he renewed his attempts to wipe out any instances of existence related to Earth, up to and including organic beast modes. Then of course when that wasn’t good enough on it’s own he wiped out individuality like any typical dictator. Then he was hit with a triple whammy of not only his old enemies returning, but with individuality AND with Earth beast modes. And so we get what we got with BM Megs and his zealotry to end all (remaining) organic existence of Cybertron. Taken this way, his characterization seems pretty congruent to me, just taken to their logical extremes from the seeds of things that enraged him back in BW.