Hi HHFan, glad that you're enjoying the game!
"it annoys me how NPCs can do some impossible actions in sex scenes. Like, if they're mounting your dick, they can penetrate you at the same time, and grab your breasts or kiss. And if there others are involved, they can grain frottage you while all this is happening"
Go to Settings, find "Multiple full sex continued actions" and select "Disable". It may not completely solve your issue, but you should find sex scenes to become more realistic.
"Also, random question, are all the trainees always naked?"
They really aren't. For speed of gameplay, it is assumed that removing clothes during combat happens really fast, unlike other games with sex-based combat where removing your opponents' clothes requires turns. The "clothes" section at the character status screen requires to special equipment, pretty much like weapons, that will be used to increased stats and sometimes grant extra abilities, but these objects haven't been introduced yet.