Focus on fixing the basic problem, as long as you're not trying to sit up the whole time you're riding (like if you're on a computer while you're riding). It sounds like you have a lot of weight on the saddle so try to offload some of that weight by putting more weight on your hands (lower position) and your feet (pedal harder). The proper saddle shape obviously helps. When I was looking for a new saddle I found that a bad-for-me saddle would be noticeable within a few minutes of pedaling on the trainer.

I can go a couple hours or more on the trainer and the saddle is not what gets irritating - it's my leg fatigue, typically cramps after 3-4-5 hours. Yesterday I totally lost track of time and ended up with 2 hours on the clock before I realized how long I'd been riding. Just so you don't think that's normal about a week ago I was looking at the clock after 20 minutes. I do stand every now and then but I spend a lot of time on the saddle.

If I sit upright on my bike I'm in serious trouble within a few minutes - bike saddles aren't designed for sitting upright. If I'm on the drops or low while on the hoods/tops then I'm good for hours.