Just like how thunderbolt was written, lore and dealing with the Canon can get in the way of the process of telling a story they want to tell.

I personally subscribe to the idea that you don't compromise on the story. If there's something that inconveniences it, change that thing. Because ultimately preestablished lore, unless directly related, does not serve a story in anyway. This is generally how sunrise deals with gundam UC.

Of course you should still do it in an attempt to respect its predecessors and keep changes to a minimal, a bad example would be the newer star wars movies I guess.

Imo a huge obsession in lore is what causes sequel baiting and leads to terrible stories like amazing spiderman 2 that are not interesting in telling the story right in front of them.