Sorry OP, I think you need to be clearer about the boundaries you set in your home.
I can certainly understand why you are annoyed, and I would be too, having a 13 year old in the house. DS new friend is virtually unknown to you, and him and not at the girlfriend stage yet, but he's been jeard having sex loudly with her.
I think in regards to you having the safe sec talk with him, maybe things became more personal to her situation than it needed to be- but given his lack of sexual experience and you seeing his naivete so far, you felt the need to point out what he (and his penis) may not be thinking about.
In your position I would discuss with his father what the expectations are of him, then discuss with him ...and even DD (in some form as to lay the ground rules in which she will need to follow in a few years time herself)
I think a good rule might be, to show your home and family some respect- that only girls who have made the status of girlfriend should really be staying over. If he isn't sure enough about her to classify her as girlfriend she shouldn't be in the family home overnight.
Maybe also that, you somehow manage to have a sex life without him being aware, each time you are at it, he needs to focus on that himself.
Get Dad to broach the safe sex talk again, less based on this girls sexual history but his own, and what an unexpected pregnancy, or STD could potentially mean... so to obviously not skip condoms.
Also outline if she's going to be welcome to stay again, what that scenario will look like...
I'd also be a bit 😒 about the text she wrote from him to you.