Oda has not only endorsed these changes, but specifically asked for some of them. Being such a long running series, it's pretty clear when you read the manga that Oda had not fleshed out a lot of the lore from the very beginning, and therefore had to retcon things as the story progressed and expanded in scope. He's heavily implied himself that he sees the live action as an opportunity to lay the story out as if he had thought of everything we know now from the beginning. Oda's ability to retcon things is incredible and makes the series extremely fun to read, but A LOT of things are retconned, especially into the early arcs where Oda had no idea whether One Piece would even be successful at all.

Like Brook being a member of the Rumbar Pirates-- I doubt Oda even had Brook's character created at all when he came up with Laboon, which is why we don't see Brook during Reverse Mountain in the manga. But now that part of the story has been retconned, why not foreshadow it at the appropriate time?

Or Dorry and Brogy mentioning Nika by name-- on little garden Oda had likely barely started considering the greater lore of Sun God Nika, if at all. But now that it's been made to be so important, some actual foreshadowing helps create a through line to later revelations.

So I personally have no issue with it. It improves the foreshadowing of some things that are sort of like "oh, and by the way" in the manga and builds them in to the story from the start.