Yeah, I get feeling nonplussed by this when not much really happens, but it's 200% consistent with the kind of fiction you find in 90's lesbian magazines from Japan. It has more to do with queer counterculture art than yuri as a genre. It's not really about girls falling in love with each other, it's a story about embracing your sexuality, moving on from your small-minded family, being proud of yourself and your community, and learning not to expect too much from curious straight girls. That stuff's a little old hat for us in 2017, but I think it may have been a lot more transgressive and inspiring in 1997 Japan.
Aside from that, though, I feel like it's trying to challenge the idea that heterosexuality makes any more sense than homosexuality. If the common view of lesbian relationships at the time was that it's a bizarre and delusional diversion from the Proper Social Responsibility to meet a man and get married and the Proper Woman's Destiny to be a mother, then the manga asks whether those things are actually any more obvious and sensible by themselves, or if we're all so steeped in those concepts that we've just become desensitised to how weird they actually are.
Natsumi stumbles around the lesbian bar like it's a zoo, fascinated by these strange creatures she's discovered and their peculiar ways, but her fixation on her own ability to procreate - which she doesn't even understand! - and her fetishization of conception, is just as strange and contradictory, if not more so. She happily shows off her "egg" as a symbol of her fertility, a symbol of her womanhood as a whole, as if it's something marvellous, and then happily flushes it down the toilet. Because we don't actually think of it as something magical. Most women ovulate, and the vast majority of the times that they do, it's not a magical symbol of femininity and a deep source of pride, nor does it actually produce a child. It just goes in the waste, end of story. The manga might be pointing out this contradiction between what we say is valuable about womanhood, and how we actually treat those things in day-to-day life.
The random guy in the cafe, I'm guessing, is supposed to reflect the idea that most guys are kind of confused and grossed out by the whole process, and might not even care about the mythologising of conception and pregnancy at all, but are still willing to go along with it as long as it means they can get some.
In the end, Yuki isn't just cheerfully waving goodbye to a weirdo freeloader, she's cheerfully waving goodbye to her lingering apprehensions about her role as a woman outside of motherhood, having come to understand that, despite what her family taught her, being gay is no more perverse than being straight, and straightness was never going to satisfy her anyway.
At least, if I wanted to read a bunch of metaphors and symbolism into the story, that's what I'd come up with. I feel like it more or less fits as a response to Japanese cultural norms at the time, coming from an offshoot of second-wave feminism (the magazine says "for womyn" right there on the cover, after all) and is consistent with the tone and imagery of the manga. I don't really agree with all its assumptions and conclusions, but saying that doesn't really mean anything when I basically just made it all up off the top of my head without knowing much of anything about this stuff to begin with, lol.
This is a completely legit close-reading. Seems entirely accurate, in any case. The critical view of heterosexuality is there, at least that it can be entirely perverse while paradoxically the socially acceptable way. There's a clear juxtaposition of their two lives and which one really meets the society's values. The straight, super feminine one is a pervert and yuki is a nice person concerned with what her family thinks of her.
Hell, since it's connected to second-wave, it's probably an intentional deconstruction.