It sounds to me like, from your POV, there are two things at work here... 1) The trouble with the written dialogue in the game: it's not adaptive to your station as Nerevarine and/or high office in the Temple itself, and 2) The feasibility of the Nerevarine joining or staying with the Temple once he/she knows what the "truth" is.
The first is the same issue that causes Morrowind to be such a static world. They simply didn't have the time and resources to make every questline adaptive to everything else. It's too big a job, particularly when you consider the meticulous hand-placement of almost everything in the game world. But the argument still holds... we just have to acknowledge that this is not a problem unique to the Temple.
The second is a bit more suspect, though. The very circumstances of the world you step foot into are, um... well, let's just say that they rely heavily on your ability to either ignore things, or accept that in the dream of the Godhead, all things all possible. I'm not going to go deeper than that; this isn't the thread for it. But if you can ignore some of the other crazy stuff in the game (like a moon suspended over the grandest city in Vvardenfell, poised to destroy it at any given time, save for the favor of Vehk, for just one example), then why not ignore some of the less fleshed-out parts of the Temple? And if it's not a case of just ignoring these logic-defying anomalies in the game, and you can accept that the world in TES is a fluid thing in which almost anything is possible when one knows CHIM, then why not accept that you, as Nerevarine, are just playing the hero's part in Vehk's grand design?
In any event, I disagree that the Nerevarine joining or staying with the Temple makes "no" sense. There are things that make less sense, and have far deeper implications. In my humble opinion, of course.
If RP is a science, someone else is the Dean of the College! I have a lot of my own ideas about what RP is, what immersion means to me, and how it all interacts with my view of the Universe, to be sure... but truly, there are some folks on these boards that have forgotten more about RP concepts than I'll ever know! And the lore folks... man, I could learn so much more! But as humbly as possible, I must say, I do like the sound of "The Vegtabill Postulate"! Ha ha! Kind of roles off the tongue, doesn't it? Or is that just me? Yeah... probably!
Thanks!