I mean the game literally NUKED Shady Sands AND New Vegas. They're basically saying the NCR doesn't exist
This is my major problem with the show. Reseting California so the show could happen is 100% pure shit. If you wanted a semi-lawless wasteland, there's so many less extreme ways of doing that. Set it earlier in the timeline, for example. Don't set it in California. Give the characters a reason to move around! There's only so much that NCR can control. They didn't even have very good control on things in Fallout 2, for example. Or here's a thought, explore the NCR bringing civilization back. It worked for Gene Roddenberry's
Genesis II even though that show was scrapped in favor of making a
Planet of the Apes TV series. It was revamped to make the series
Andromeda, which was moved to be a space based sci-fi. But if you haven't seen
Genesis II, you're missing out on some good post apocalyptic world building. There were also two sequels produced for television. Here's a bit more on that:
https://ripjaggerdojo.blogspot.com/2019/08/the-many-lives-of-dylan-hunt.html
not to mention continues to bastardize the BoS lore, by making them into even more cringe-inducing, paladin-like heroes.
The big problem with this is that they nuked Shady Sands. The BoS could have easily become "paladin-like" heroes under the NCR since the Big Fear(tm) the BoS had was that mankind would destroy themselves again with technology. However, present a hopeful view of the NCR and you can see the BoS coming around to being The Good Guys that Bethesda seems to like to flip flop on. The main reason the BoS actually helped you out at the end of Fallout is because the FEV is an example of old world technology threatening the existence of mankind. They weren't there to be good guys. They were there because it played in to their fears.
That's not to say they could never come around. It's even suggested that they do in one of the endings to Fallout 2, if I remember right - because of the NCR.
However, if you nuke Shady Sands, guess what that would do to the mindset of the Brotherhood of Steel given their backstory? They're going to double way the fuck down on their technology hording because the nuking of Shady Sands will basically confirm their fears. They won't be the good guys at all. They'll be more militant about technology than they've ever been.