First PBP in '99 was on Shimano MTB shoes - by 800km, I could definitely 'feel' that postage stamped size cleat on the ball of my foot - VERY uncomfortable indeed!
In later years, I switched to Canac MTB shoes, which had a removable cleat-plate attachment that spread the load better (but at an increased stack height).
In 2004, I switched to road shoes and pedals (Sidi / Look)and have never (no pun intended) looked back!
You get a far increased contact area, and a lower stack height. Sure, on an event like PBP, you may well sacrifice a set of cleats walking at the controls, it is a small sacrifice for a ride that happens only every four years.
Normally, I change my cleats one time per season.