If it's touching intermittently, then you have to have something causing that periodicity.

A tight rack might warp things, but they'd remain warped. A set degree of deformation.
A rack that tightens and untightens simply isn't reasonable.
So you have to look for something that can vary.
A warped disc would do that.
A loaded rack swaying while riding would do that.
A frame flexing under pedalling would do that.
But I'd rather suspect that would have happened before you mounted the rack too in that case.

maybe the rotor is slightly untrue, and the addition of the rack reduces clearance enough so that frame flex from pedalling suddenly have become noticeable.

Or its something completely different - maybe an axle/bearing issue - that simply happened to coincide with mounting the rack