I had my B1260 without the trapdoor first... without feets... the table hot hot and the CPU even hotter. Try add at least a small heatsink to it and run it without the trapdoor (or use a custom one that allow for air to come across the CPU).
I used to have a B1230/50 MK3 for a few years and I ran it with the trapdoor on. It got hot but seemed to be happy with that.
The Apollo1260 have the CPU on the other side of the card so there's no real beenefit of running it with or without trapdoor. Probably a bit more room for a heatsink also but where's the airflow?