I had the same problem at the start. I talked to my friend who has done a lot of indoor training, and he says it worse on easy rides with low power output, because you have more weight on the saddle for longer. That said, I notice that I don’t have these pains on outside rides or on harder indoor sessions.
I found that moving around helps. Particularly, I will sit up and ride no hands on recovery sections to change the weight load. If I do this early and often I can get deeper into the work out with out the pain in the but.
A cheap gel cover worked for me. Sliding the toggle on the cover and removing it part way through a long session combined with shifting gear and standing provided enough variation in pressure to make life on the trainer more bearable. I don’t use it every ride - but do start most 90 mins rides with it on.
One thing I do when I do high volume work is have 2 different types of seats. A couple of times a year I will do a 6x50 miles on the road for an endurance boost. By day 3 my ass is pretty sore and I like my fit. So I have a different seat that I use for a day or two. It has different pressure points. By the time the new points are sore, the old ones are better and I’m back on my original seat.
I was having perineal numbness and seat soreness within about an hour on the trainer. I adjusted my low-tech riser block down. I had 2 2x6s (about 1-1/2" high each) stacked and went to 1. That extended it to 90+ minutes–and shows how sensitive (pun intended) some of the adjustments can be.
I went from a saddle with a shallow groove to a cutout, that helped. I’ve always had the trainer on a cheap, puzzle mat that I got from Amazon for under $20 to protect the carpet and makes the trainer slightly less rigid, so that may be helping. On longer workouts, I stand for 20 seconds or so at the first hint of discomfort (other than discomfort the workout causes ), that buys me another 20-30 minutes before I need to stand again. I have one pair of bibs that still gives me problems and seems to fit differently in the crotch, so shorts can be a factor, but other things like bike angle, saddle choice and bike fit were bigger gains for me.
I thought about building a rocker plate at one point, but the cat is already unhappy enough about the trainer in the middle of his living room.
I’ve had this as my trainer set up end game for a while now.
Erg mode has been a massive improvement - it frees you from worrying about maintaining an appropriate power level. Currently I read the morning news on a 45 min easy ride. Next step: I’m going to try and see whether one of ISM’s upright bike saddles (Metro/ Adamo Touring / Urbaine) with a kickr desk in front of me to lean my upper body on and use periferals would work.
If it doesn’t, maybe I’ll have to find a way to connect a recumbent bike to a trainer…
Update: was looking at building a rocker plate, but realised I don’t have the headroom (very low ceiling), so just put down some cheap foam I had lying around (about half an inch thick). That little bit of rock / flex this gives to the whole system seems to make a big difference: with decent ‘hip discipline’, basically no problems at all now