I have the same issue with most shoes- I have a weird little fat pad there.
Options that have worked for me (narrow heel, wide forefoot):
Kenn Mid Voygeurs- this avoids the issue of the shoe ending at the same height as the place it rubs, but relatively heavy
Asics 4E trailrunners. At first I thought they rubbed there, but as I tested them out at work (on my feet most of the day) I found I ceased to notice it. I wore them on a recent 5 day Sierra backpack with zero issues.
OluKai training shoes- got them at REI and wore them on two overnight backpacks- also zero issues. REI is sold out but Amazon has them. More support than they look like they should have.
If you have a narrower foot than I do, you might look at Keen running shoes.
Good luck- took me 8 months of trying on various trail runners to find those two.