This is a problem I have had with numerous headphones and it's so hard to get info on it because so few people seem to have the issue. I didn't think I had larger ears, but clearly larger than average, it's always the hard ridge of cartilage on the inner part of the ear for me, moreso on the right than left.
I sold my Meze 109 Pros because, despite liking their sound, the pads were just open to the metal grate driver cover and my ears would rub against that which drove me crazy. HD6XX I noticed they do as well but they actually have a thin piece of foam covering their driver and that does just enough to soften it. When I got my Auteur Classics, with the Auteur pads I still found if I wore them more than 30 minutes, those ridges on my ear would start to get sore from pressing against the driver cover. What I ended up doing with my Auteurs was a bit random...I got ZMFs suede 6XX pads on a whim, which are thicker than the stock, and I ended up using the foam 6XX backing in-between the Auteur driver housing and the pad backing. So my ears still touch, but there's just that little bit of padding there so I can wear them for hours comfortably. I also don't notice any sound difference with them (I'm sure someone with keener ears than mine could, but I don't).
Anyway, sorry for a bit of a ramble, but I appreciate you noting this because I was almost decided on the Atrium Closed as a second ZMF and upon realizing that the stock pads are the Caldera Thins and others like the Caldera Thicks aren't recommended for their tonality, it's really shifted my focus over to the VC and it's larger variety of [thicker] pads (this isn't the only reason, but it was an incredibly tight race in my mind and I think this is probably the deciding factor).