Is RI contagious?
Yes, through cross contamination.
Should my bps be separated?
Yes, BP should not be house together to start with and each individuals should have been quarantined away from each other (different room)
Is the reptile shop guy correct that this is something that they can get over naturally?
No RI do not heal on their own, RI require to be treated with anti-biotics.
Did I make the right decision in letting the reptile shop house my bp to make sure he's healthy?
No obviously from the answers that were given by them show that they are not that knowledgeable.

If the BP you just purchased has a RI you should return it to the, it is completely unacceptable that someone would sell a sick animal.