Because we don't have a girlfriend.
"we" are not necessarily interested in having a girlfriend. We could be interested in having boyfriends. One or several. Or none at all. Or someone not specifically characterized by a gender. Or by another gender not listed here.
Genuinely curious, then why not leave it be? It's just a joke as you admitted, with no ill intentions, based on a stereotype that's mostly based in reality. Stem fields are mostly sausage fests. It's also quite a stretch framing it as "exclusionary", it's a self deprecating joke.
So in this case, I don't think there's any reason to believe there was an exclusionary intent, and I don't interpret GP as saying that or as calling GGP out, but there may be an exclusionary effect, and I give it's totally reasonable for GP to respectfully add this footnote to mitigate any unintended negative impact.
Some may say this is being a wet blanket or ruining the humor, but people always call you paranoid or a safety Sally or whatever when you try to mitigate unintended harm in any context; you learn to ignore it.
I used to be involved in a biology lab, and people loved to stand on these rickety tables that fell apart at the drop of a hat. So I would bring them a stepladder and politely insist that, if they were in my lab, they were going to use a stepladder. They called me a safety Sally everytime. Doesn't mean I was going to let them smash their heads on the cement floor.
I tried reframing your question to, "how would you have made this joke, preserving the slight", but the joke isn't to my taste personally, which is only a problem if you ask me to rewrite it - I'm not expressing this as a criticism of the joke, I'm just the wrong person to ask, because when I try to imagine how I would've made the joke, the answer is I wouldn't because it isn't my sense of humor.
I don't really have a problem with the way events unfolded with joke being made & getting a footnote. That honestly seems fine to me, I don't think it requires tinkering.