We don't really know that's how things are normally done.Zaranites, which we KNOW serve on Federation ships alongside humans as they are seen among the crew in TMP, are fluorine (which reacts violently with oxygen and hydrogen) breathers. They also wear masks which filter the light as the standard setting for humans is too bright for them.
We see Zaranites on earth wearing the masks, to be sure, but I'm certain that most of their work is done in zaranite-friendly facilities, where the masks are not required. Easy to do if you've got entire cities to deal with, less so when dealing with a relatively small ship.
We do see at least one Zaranite on the Enterprise, but remember, the Enterprise is being launched ahead of schedule and that they're struggling to come up with crew. Perhaps the only person qualified for some job, or the best qualified in any case, happened to be a Zaranite. And that Zaranite would be required to live "in-mask" or the time that the ship would be on this emergency, but would not be permanently assigned. (Later films do, at least by omission, seem to confirm this, don't they?)
Further, we don't know that Zaranites breath fluorine, really, from anything seen on-screen. Nor, for that matter, about the light requirements. I see no major issue with this, mind you, except that for the purposes of ST-TMP, it seems unlikely that they'd have had the opportunity to install that sort of "non-standard environment" prior to the early launch anyway, doesn't it? They were struggling to get the ship flight-worthy... and this crewmember wasn't one of the most critical people on the ship, was he? (I mean, we never MET the guy, after all!) So, I'm not 100% sold on the definition you just gave me, anyway.
But if this WAS the case, this crewer must have been entirely irreplaceable, or they must have set him up in some special "ambassadorial" cabin specifically designed for short-term occupation with "alien environmental needs."
In any case, it remains impractical to have crew assigned who have dramatically different (and incompatible) life support requirements, and all later Trek supported that idea, as we never see another one of these guys on any ship we see.
Ignore, for the moment, what it would mean to this one guy... imagine him serving on the bridge and his fluorine tank springing a leak, causing all the human crew on the bridge to need to evacuate. It just make no sense.