Disk brake wheels - multiple wheelsets
This is normal for using different wheel sets. Not all wheels are precisely the same.

I have a similar thing with wheels on one of my bikes.

Learn to align calipers quickly it's a simple process (with wheel on):


Loosen calliper
Squeeze brakes twice
On third time hold brake in
With brake held in re tighten calliper


With practice should be about a minute a wheel.