his perception of other humans and the lens he looks at them with is constantly being altered
Not really. Perks give him insight into a lot of things, forcing him to reevaluate his viewpoints as he learns more, but one of the viewpoints that withstood all the perks is Joe's opinion in other people and humans as a whole. He never started to think of Ms. Gartenberg as younger than him, never though less of Doug just because he is (relatively) worse at organizing people, and he even managed to connect with Theo by just offering genuine understanding of his struggles, something he wouldn't be able to do if he truly started to disconnect from human experience. Perks have no sway on Joe's perception of people. The closest perk got to affecting Joe's perception of humanity is Master Builder's "human tech is rubbish" effect, something Joe stumped out and never returned to. After that, Joe never thought of anything "human" as separate of himself (aside from that one time with Butcher, but that was more him taking every opportunity to belittle a person he already despises than anything else. Joe is a bit petty, it is hereditary.).
And that is the thing. You word your questions as if Joe is not human. But, while yes, some disconnect happens, it is prudent to remember that Joe works on eliminating it and remaining human. It's the whole reason Aisha being around works. It's impossible for Joe to start thinking that humans are unfit to be romantic partners for him, because that will require him to think of humans as something completely disconnected from him, either lesser or too different to have commonality required for romantic feelings. And Joe puts too much effort, Apeiron level effort mind you, into being human for such disconnect to ever happen.
The real question is if Joe too work oriented at the moment to entertain a romantic relationship. Or any kind of social relationship for that matter, he did almost refuse that non-romantic coffee meet up under the pretence of "We have too much work to do". Haha, Joe has a personality that could lead him to became just as socially isolated as Armsmaster, that tracks. Good thing that duplicates and the team are ready to beat him with sticks whenever he's trying to be too "efficient".