I've been using Speedplay for years. I did have this problem, but it was from wearing Sidis that were too narrow for my average width foot. Then, when I got my new Shimano shoes, the special molded to your own foot insert was so thick and awful (my LBS thought I was nuts), I wore my shoes for 2 weeks without any inersoles, and then went out and got the blue Superfeet ones. I need thin, thin, thin inersoles. I seem to have this issue with my hands, too, hence the need for gloves with no padding or gel. I can't stand anything thick or tight on my extremeties when riding, as it causes immediate pain and swelling, even in cool weather. Not swelling that is visible, no medical cause. Problem solved.
I do get the hot spot a bit, still, with my mtb style shoes and Frog cleats, but only on 40+ mile rides, on the foot with a bunion. But, it was much worse with spd style pedals that had a platform.
2015 Trek Silque SSL
Specialized Oura
2011 Guru Praemio
Specialized Oura
2017 Specialized Ariel Sport