I suspect the reason Viera and Hrothgar don't pay less for Mogstation glamour despite being unable to wear the hats is, as other people have said, because you're buying the glamour items and they don't care what you do with them. You don't get a refund on hats when you fantasia from Au Ra into Viera, you don't get a refund on the female glamours if you fantasia from a miqo'te Seeker lady into a giant Roegadyn guy, etc. And you're free to buy the male glamours to put your retainers (or Kai-Shirr) into them, etc.
Beyond that, I think (though I'm not sure) that these particular sets actually pre-date the Viera and Hrothgar, as I think they may have been older ones exclusive to one of the Chinese or Korean versions of the game that are licensed from Square and run by other folks (and who are running considerably behind the global version in terms of what patch they're at).
Doesn't mean they shouldn't have probably adjusted the items for Viera and Hrothgar when they brought the items across into the global game, mind you. Though for all I know, the potential legal complexities of licensing content back from people who license Square's content and then add stuff to it... maybe they're not allowed to change the items, or whatever. (I certainly saw weirder contract conditions when I worked in the games industry, so.)
But all that aside, while I get not wanting to go back and retroactively fix all previous headgear for Hrothgar and Viera—which was a cost folks pretty much knew was coming going into the addition of two new races (or really, one new race that just is split into gender-locked variants of two races)—I do feel like it's a little disappointing they don't seem to be making the headgear work on new stuff in general going forward (even if I understand the designers probably having some frustration with how you'd handle Viera ears for some of them).
I certainly do think selling pieces of sets would be great; I have never, that I can think of, used an entirety of a set at once. The most I've done, I believe, is two pieces of a specific glamour set at once; my long-time WHM glamour was the Lightning chest (dyed white) and boots, along with the Leonhart pants and gloves, and the Nezha Lady headpiece.
And while I use the Nezha Star headpiece so often that it's basically part of the character's design at this point, I don't think I've ever actually used any other piece of that glamour set.
So being able to buy the individual parts of a glamour set would be exceptionally nice.