There’s a few things.
Some shoes don’t match some pedals very nicely. The outsole of my Recon 3s doesn’t contact the body of my Shimano pedals so it gives that standing on an ice cube feeling. (I’m quite light and the shoes are quite stiff so although it feels a bit sketchy it doesn’t cause comfort issues for me).
Shoe stiffness, as above. I suspect you can put rather more force through your shoes than the average guy, so unless you’re using super stiff XC disco slippers, you’ll be getting more sole flex than typical.
Have you checked the ends of the bolt threads aren’t protruding inside the shoe at all?
Even though they’re not the best fitting shoes for me, I find the combo of Shimano shoes and Shimano pedals the best overall solution as they work together very nicely.