as far as I know, yes.
ANY sex scene from what I can tell causes you to lose your virginity. I haven't exactly tested it, but I had a few mistakes on my run(s) for Logan too and they all made me have to go back a lot of saves lol
It's always satisfying when you finally get the person who's playing hard to get. I, too, had to reload certain saves because of mysterious reasons where I lost a virgin status somewhere.
The Virgin route was definitely worth it, but I hate how you have to get really flirty to the point where it's almost borderline cheating to get other quests from other people, specifically Bernard. I love Bernie to bits, but I don't like how I have to obtain 2-3 hearts from him to unlock Caleb's quest line. I stopped at 2 hearts, 'cause it involved a quick kiss with him.