Not enough space to adjust the caliper
Depending on your brakes and their design, you may not want the rotor centered.  

If both pads move when the lever is squeezed, then center position is correct.  However, if you have one fixed pad and one pad that moves you want the rotor to be as close as possible to the fixed pad (without touching/rubbing) so that it bends the least when the one moving piston is engaged.

Most brake manufacturers design their brake calipers with slotted grooves so that the brake unit can be adjusted.  Some Magura breaks are an exception to this and require you to adjust the rotor with spacers.  However, for most disc brakes, if you have the proper adapter and true rotor, these slots should be all you need to adjust the unit properly.