Yeah, that's the other side of the argument on the Forums. Many say that All Roads is non-canon, and that the inclusion of horses was an error. I'd rather not get into that argument here, as I don't believe it's too much of an issue, I just thought that I'd point out that there's a bit of controversy surrounding horses in the Fallout universe.
Again, I have absolutely no issue with the inclusion of horses in this RP. If they aren't extinct then I'd agree that they're likely bred and used extensively in the NCR.
Edit: I've just read your edits. I don't think the horses will be an issue, and would love to see you stay. Chances are nobody here cares about the issue too much, and I'd love to see your General and his troops in the RP. Don't let it bug you.