langclegflavoredbananamush that's an interesting example to bring up!
One thing I've noticed over decades of watching Star Trek is that it's not really sci-fi in the sense of exploring what might be; it's actually mainstream TV for a mainstream US audience which tells you far more about the American politics of the moment in which any individual episode is made. And what's more, it unwittingly tells you a lot about the tensions between the image the US wants to project of itself and the US as it actually is.
So old-era Kirk et al - prime directive, not interfering with alien civilisations (again, how America of that era would have liked the world to see it, rather than how it was, fresh out of the Vietnam war); Captain Janeways era - realpolitik comes to the fore, politics and space exploration is a dirty business and sometimes otherwise good people have to get their hands dirty in pursuit of the greater good (against a backdrop of Gitmo in the real world).
So (as always) all this choice of thing to make a kerfuffle about in the plot and in the accompanying press releases tells you is that this is a hot topic in real-world American society, and this is what the programme makers think the "politically acceptable" real-world read on this topic is.
And as with your Quark example, this also reveals interesting things about the real-world prejudices of the programme makers, some of which they don't actually intend to reveal!
I think the other thing that's been implicit in sci fi like Star Trek for a long time is the "hearts not parts" mantra. Some of this was well intentioned (cross-species relationships in sci fi often functioned as a somewhat clumsy metaphor for inter-racial relationships at a time when those weren't accepted by mainstream US culture - though I think the Kirk-Uhura kiss achieved more in this direction than any amount of humans marrying Klingons or whatever). But I think there's always been an odd undercurrent of biology denial - I mean, why even think an alien would have the right bits to make romantic/sexual cross-species relationships possible, much less desirable?