I have read the OP's posts but not the entire thread.
So the dad of a 17 year old girl is upset that she is telling him she is going to her BF's to study, but is then not studying and somehow he seems pretty confident that they are having sex at your house. By your own admission you do not mind if they are having sex as they are consenting adults.
Crumbs, I really see both points of view.
I honestly don't think you are doing anything wrong. You are respecting your son and his GF to determine for themselves how much they need to study, and recognising that in a healthy relationship sex is to be expected. It sounds like you have a really good relationship with your DS, probably as a result of your excellent parenting.
I also honestly sympathise with a single dad who is probably quite stressed about the fact that (in his eyes) his beautiful princess who has done so well all her life is now spending all her time with a BF that he doesn't know, and is not doing the studying she says she will do.
We don't know whether she has told him they are having sex or if he just assumes it, but I currently have a 16 year old DS and a 15 year old DD, and if in two years time I found out they were both having sex with their partners I really would not worry about my DS, but I think I would feel quite stressed and protective about my DD. And a big part of it is the risk of pregnancy yes.
But probably in a few months she has gone from being his little girl who was always at home and did her homework and got lots of grade 9s, to being someone he feels he doesn't know quite so well, who spends lots of her time at her BF's house, doesn't do the studying she said she was going to (apparently) and instead is getting distracted from her studies and potentially risking pregnancy by having sex with your son (in his opinion at least).
I know that most people on here are saying ignore him. I would say speak with him, sympathise with him, but also be very clear that you will not be checking on whether or not they are studying because you trust them and it is up to them to manage their work. If he wants to reduce the time they spend together to make sure that she gets her work done at home, then that is up to him.
You are not doing anything wrong, but I understand him worrying.