True, most people have their saddles too high. Then again, just took my bike off the trainer into the real world this week and had to raise the seat. Best solution if you can afford it — 1 trainer bike+fit, 1 outside bike+fit.
A fixed trainer is less forgiving of those marginal setup issues. You might be able to move around and adjust outdoors but not on the trainer. If you have a super stiff bike, though, once you get the fit correct it will be more comfortable on the trainer than it is outside.
I’ve got an NK1K & it can ride a bit harsh outside but it’s actually pretty comfortable on the trainer.
It’s funny, I’ve found the reverse is also true. My trainer bike is really stiff and went out of commission for a bit, so I substituted in my Canyon Endurace for a week and had terrible saddle sores. My opinion was that all the frame flex was translated directly into the saddle which acted like a windshield wiper on my hind bits. Ouch.
Also, some trainers are not level, i.e. my elite novo force has a discrepancy with how high each wheel is of the ground. The back wheel is not at the same height as the front one with the stock front wheel holder in place. Obviously a design flaw. What it does is it tilts the entire bike so you need to correct that with your saddle height and tilt. Once you go outside you then need to change the whole thing again… Bit of a pain in the ass
It can actually be tilted in any way. If the trainer doesn’t have flaws like mine you need to make sure that the surface on which the trainer stands is level. If you are having one side knee problems then it potentially could be due to the trainer not being level left to right.