If I use raf legitly with my soon to be bots and then turn on the bots afterwards, would the fact that they are raf accounts increase my chances of being banned once I am botting?
Of course I can't say 100% no, only blizzard could tell you that. But there is no reason it should increase your chances of being banned. These two mechanics have nothing in common, does every botter use RAF ? no, is everyone who is using RAF bot ? no -> blizzard has no reason to investigate. And since your RAF time is legit, there is even less reason. Don't worry about it.
I think maybe if one of them gets hit with a banned and they check accounts associated to that one you may get the other banned to? im not sure if blizzard checks associated accounts or if so how often when they ban an account