If I install my BMS tune before my intake will that make any difference?

 

I can't say for sure with the IS, but from what I have seen with other tunes, probably not in the long run. The ECU is always adapting timing, boost, fuel trims, etc. based on knock, intake air temps, and other factors, so the order of operations shouldn't matter, especially if your tune is designed to be used both stock and with an intake.