Some of mine:
1. There are a lot more human mutants around, we simply haven't seen them yet. We don't know about most of NA yet.
2. Vree was right about the bio-genetic weapons, but wrong about more mutations caused by those. She has simply not seen those mutations yet, because most mutations in the West Coast were caused by airbone FEV and rads, due to being near West Tek.
3. A single human race is pretty much done, for now. Its a world of mutants now, even the humans are just a human subspecies, as the Enclave discovered. "Humans" are the majority, but there are plenty of human mutants from a variety of causes, everywhere. Its more like that part of pre-history where homo sapiens lived onside Neanderthals, Denisovans, Florensis, etc. Not all of them are sterile, deformed monsters either. Its not Gamma World tier, but mutations are common and many can even breed with humans (cue racial panic).
4. East Coast FEVs are inferior versions compared to the one tweaked further by the Master. This is why East Coast Super Mutants are almost all psychotic green retards eternally growing, while West Coast Super Mutants are generally smarter, saner and stop growing
5. Super Mutant Behemoths aren't created purely with age. Fawkes is two hundred years old and is pretty normal. They are a special mutation within the mutation. Its just that East Coast mutants this old tend to be weak enough not to make it. Survivorship bias, in other words.
6. The original endings of Junktown are canon. This is why the Vault Dweller's diary seems to not be entirely happy with his actions in Junktown. Killian became a tyrant and Gizmo was actually the better choice.
7. The Gun Runners moved to the Hub after FO1. They returned to their old Fortress in Boneyard, later on, but staying in the Hub and becoming the top weapon manufacturers of the Wasteland makes more commercial sense.
8. Elder Lyons is a pretty cool guy, but he is a horrible strategical commander and that's why the D.C Chapter is losing: Because these idiots keep fighting urban warfare against genetically enhanced Super Soldiers, rather than seeking their HQ for one surgical strike or engaging them in the open outside D.C. He's Father Elijah-tier of sucking at warfare.
9. The reason the Chicago Chapter (the Brotherhood from FOT) was "off the radar" to Lyons and co, is simple: They saw a bunch of armed Brotherhood personnel coming from afar, and thought this wasn't an expedition or diplomatic mission, but the Western Elders sending a strike force to eliminate dissidents. Remember: The Airships were deliberately faulty and meant to kill or strand them.
10. Most of FOT's events happened. Not 100% how they went in-game, but they did. Calculator might have not been in a Vault at all. Mistakes like "BOS came from Military Vault" are actually in-universe mistakes because the Brotherhood sucks at preserving history.
11. Bonus: Gammorin/Latham was going to suceed in curing mutant sterelity, given time, but thanks to the Midwest BOS, they never got that time. Why? Because its more tragic that way.
12. The Super Mutant Army was made of a few thousand members. At least a thousand, possibly 1000-3000. In short: There are as many Super Mutants as the plot demands, but not TOO many Super Mutants.
13. Reservation exists as a vassaldom/protectorate of Caesar's Legion. It was pretty heavily defended and in radioactive land. Caesar ran the numbers and it simply wasn't worth it to lose thousands of men to conquer radioactive shit land around Los Alamos. It likely makes a living by supplying the Legion with weaponry and tech. Its like Ghoul North Korea over there.
15. Born Ghouls are a thing, and by 2281/2288 there are LOADS more than in Van Buren. And they already discovered Born Ghouls can breed true (at least with humans). Reservation is playing the long game and waiting the Legion to collapse.
16. Born Ghouls in VB were meant to be a way to keep Ghouls around in-universe as a viable, growing race. Belle was going to be the "Eve" of Born Ghouls, with the Prisioner as their "Adam". Its why they grow so fast - so they could have plenty of those for the next few games. Eventually, "Old Ghouls" would become a rare thing.
17. New Arroyo is independent of the NCR.
18. A big part of the Legion's economy is actually mining and selling Copper. Arizona has some of the biggest Copper reserves on the planet.
19. Trinity Test Site (where the first atomic bomb was detonated) is considered a holy site to many weirdo religions - atomic worshipers, death cults, doomsday cults, even some tech-cults. The Legion allows them do all sorts of weird pilgrimages and shit, because it brings in money. Hell, some Mars cultists might consider it sacred because Mars sent in the nukes to destroy the world.