I say it shouldn’t but probably will matter knowing this sim but if you set up different profiles for your controllers and don’t mix them up then you should be fine. I’m not certain about syncing between PC’s but since SU5 the MSFS store version is supposed to be a play anywhere title it should work on any PC or Xbox if no one else is using your other set up. If you’re already on Steam I suggest switching to store (although I doubt you’ll get a refund).