I have an OEM wheelset with Formula 6-bolt disc hubs, and a pair of Zipp 303S wheels which are centerlock. I am using different rotors as well - the Formula hubs have Shimano RT56, and the Zipp hubs have Shimano XT (MT800). Out of the box there was some slight rubbing on the Zipps. As others have noted, it's fairly simple to re-center the caliper, but it's also fairly simple to add shims to the rotors to get them aligned between different wheelsets. In my case I set the calipers to align with the Zipps, and added shims to the Formula hub's 6-bolt rotors. The shims cost just a few bucks, took just a few minutes to install, and now I'm able to swap wheels with no rubbing and no need to touch the brakes.
I have noticed that I need to do a slight RD barrel adjustment when swapping between these wheels to keep the shifting running cleanly. It works without touching it, but there is some extra noise on the lower gears. I'm running identical cassettes on both sets so there's either a slight variation in cassette manufacturing, or the freehub bodies are slightly different. Either way - after I swap wheels, I'll run the chain up and down the cassette a few times, and a half turn or so on the barrel seems to sort it out. This only takes a few seconds and is no big deal.