What does the tube of caulk say about paint types? They'd know better than pretty much anyone here. However, I'd venture to guess that a decent exterior latex paint would be acceptable and should not be a problem with typical RV exterior components.
By the way, the air conditioner is designed to not be caulked where it meets with the roof. There's a foam gasket between the two for sealing; if it's leaking, this should be replaced. (If it's not leaking, all that is required is to occasionally check that the bolts holding the top unit in place are slightly snug. They do not need to be tightened down very hard; it's fairly easy to overdo it.)
Most everything else that pierces the roof needs caulking or sealing from time to time; the products generally used are Dicor self-leveling lap joint compound or Eternabond tape.