Where we live we have pelvic floor specialists. They are specially trained for that part of the anatomy and are able to manipulate internally. I do refer some clients to them when there are issues such as you describe. It is worth checking out if nothing else seems to help. Usually they are registered physiotherapists.
I've been riding for over 40 years, and for nearly 30 of those years have suffered severe seat bone pain. It started when I was 25, after 12 years riding. Every time I got in the saddle, I would experience pain after a couple of minutes. After a long ride I would be left with sore, swollen patches on each seat bone. I tried different saddles, seatsavers, padded knickers, the lot. Nothing really helped, so I just put up with it, but it meant I couldn't do the really long rides I love. About 5 years ago, it gradually improved and after a few months I was fine again. Just recently, it has started again - only on longer rides at the moment, but I am terrified it will come back full force.
During this time, I was not able to wear ankle length boots because a similar reaction occurred on the backs of my lower leg where the boot touched, severe pain and swelling within minutes.
I am certain it's not muscular, so chiropractors, physios, etc. will not help. I think it may be something like an over-active bodily response to pressure in the bones. If it does come back, this time I'm going to see my doctor and hope maybe there is a steroid or cortisone treatment which will help. I desperately don't want to go back to the painful old days.