To me it seemed like the showrunners were far better aquatinted with the games than most writers are with their source material. A lot of things get changed in writers rooms for practical reasons, like moving Shady Sands next to the Boneyard so the protagonists don't have to travel over a hundred miles over mountains to visit it, or changing Novac to fit with the filming location and action sequence. For the most part, these retcons don't absolutely break the stories of the past, while providing enough benefit to the current story to be worth it.
This isn't to say that everything works, but what doesn't work for me has less to do with lore and more to do elements just not working. My biggest problems with this season stem from the writing not being as tight as the first. I'm also worried that Nolan and Joy will make the mistakes they made in Westworld where they didn't have a narratively compelling long term plan.
At the same time, none of what they've done with the factions surprise or disappoint me. The Brotherhood are jackasses who only had benevolent leadership in 3, the Legion were doomed without Caesar, and House was an eccentric weirdo who thought he was more important and capable than he really was.
Most controversially, the direction of the NCR makes way more sense than some fans want to admit. The NCR has reflected American liberal democracy in every game in which it prominently features. In Fallout 2, it's a promising force with cracks in its ideals, mirroring the perception Americans had in the late 90s. In New Vegas it's stuck in an imperial quagmire while wealth inequality weakens the country from the inside, mirroring the war in Afghanistan and the neoliberal post recession "recovery." Finally in 2024, on the eve of America's collapse at the hands of oligarchs, liberals who refused to change, and fascists who took advantage, the NCR has collapsed at the hands of Vault-Tec, the NCR's established problems, and the Legion and Brotherhood (who fuck it all up because they're fascists).
Honestly, them going in this direction is more compelling, better commentary on our current politics, and more in line with the best that Fallout has to offer. I think a lot of people were too attached to their favorite factions to see the bigger picture, and the writers not doing the same has made the show better.