Hello again!
Those questions only appear during "chapter 1: the fundamentals" if you ask your companion "if she's nervous." If, instead, you "tell her you're ready to begin," you'll never see them (regardless of whether you're on your first playthrough or your tenth). Maybe it wasn't the best design decision but I figured, if a player wanted to jump right into the naughty bits, they should be allowed to.
If you, personally, never see the option to "ask if she's nervous," or if you do select it and don't see the choices that come afterward (e.g. "why she wants to join the Academy", "her opinion on training"), let me know! I've tested it just now and it works for me, but that doesn't mean it works for everybody.
Thank you again for your time and attention!
-Lars