I have this problem, too. I can't wear my beats noise cancelling headphones for too long or the pressure starts to hurt.

The Apple web site states that the new AirPods have an internally-facing microphone, as well. I wonder if that will help. They're touted as being unnoticeable.

I agree. Thankfully the Bose app allows that to be turned off when it gets to be too much for me, though the office is worse without the Bose cancelling, at least it stops killing my brain.

Do they physically hurt your ears, or is it just some personal discomfort you can get used to?

It's somewhere between a headache and physical discomfort. Hard to describe because I've only ever experienced it with active noise cancelling (over the ear) headphones and I gave those up 5+ years ago.