I've never dissected a human cadaver, and I have no advanced degrees in medicine or physiology, and I naively figured there was no muscle cushioning my sit bones (ischia?) from a saddle. I'm not convinced either way, but it seems unlikely that muscles are useful bottom cushions for cycling.
Apparently the stuff that mainly cushions your ischia bones are the
ischial bursae, which are "small, fluid-filled sacs that cushion your sit bones" (google AI).
My uneducated hypothesis is that sitting a long time on the saddle squeezes fluid out of these sacs, and occasionally pedaling out of the saddle allows the sacs to plump back up. As soon as I feel a hint of butt soreness, I get out of the saddle for at least 30 seconds. This has always worked for me, and I'm on the lean side of lean, so there's not a lot of extra tissue down there.
According to the Cleveland Clinic, if you sit a long time on a hard surface, you can get
ischial bursitis. Sounds exactly what a cyclist gets from riding in the saddle for too long.
Edit: Here's a diagram showing those ischial bursae.
Source: Cleveland Clinic