Well that could be the "rub" If your wheel can't be reliably put in the fork DO without checking clearance, something could be wrong, caliper alignment, bent fork legs, off set rim from hub, debris in the DO, loose bearings....

I don't blindly drop a wheel in the forks. I hold the wheel in the DO with a finger around the rim by the brakes. I can feel if the axle is touching both DO bottoms or not when I center the tire in the fork based on the center of the tire and the brake mounting bolt/nut or hole in the fork as a reference. I then use the QR to close while looking at the centered tire in the fork.

Brakes are always the last adjustment in my approach. Wheels not centered to the frame reference points causes ride problems. Once I went for a 30 mile ride on the Colnago with a new set of used wheels. I decided to try hands free coasting. That is when I found out that both wheels were not centered. I had to cant my body slightly to ride hands free. I think it required two or three turns on the spoke nipples to get centered.