There's zero difference in performance between 6-bolt and centerlock. I think most higher end hubs seem to be moving to centerlock, but there are (and will be for a long time) still lots of good rotor options out there for 6 bolt, so I wouldn't see that as a limiting factor. There is no difference in terms of rubbing.
For reference, I have two wheelsets on my gravel/CX bike - one has 6 bolt, the other has centerlock. They both swap on the same bike with minimal adjusting (I did have to shim the 6 bolt rotors which is simple) and the only time I notice any difference is when I occasionally check the torque on the rotor bolts, or need to remove a rotor for some reason (which isn't very often). I prefer centerlock because they're a more simple design.
On hubs, there's a big difference between Shimano's cup and cone setup and something like White Industries, which uses cartridge bearings. I have owned Shimano Ultegra hubs in the past and much prefer the cartridge style setup, as they're more maintenance-free.