Wow. Really impressive find - much thanks for putting it up!!
I can sorta see why it's rejected:
1. How to make Spock look 78 years younger
2. Gimmicky in a sense to get at ratings by bringing back Spock-a-rama
3. it's still doing a sequel, and to such a revered story (again, low hanging gimmick) and everyone remembered just how awesome "The Naked Now" was received
4. Using TOS as a crutch, which Roddenberry wanted to avoid
5. To keep it simple: $pock might cost too much, with other episodes suffering as a result of budget loss
And yet:
1. It's thought out fairly well, as to why the thing would be guarded
2. Poses a reasonable and interesting mystery
3. Especially prior to TUC's development, Spock being scientific and not becoming an ambassador (a la Sarek) still feels more apropos but anything's possible
4. Only Torme could pull something as grand as that off, especially given the relative infancy of TNG at the time
"Unification" was trying to homage TOS after taking 3+ years to define itself, and as a result everyone in it manages to suffer. Spock was reasonably well used but could have been much better. Opera singing was silly and almost like Star Wars in a warped way. Data neck pinch is a far worse gimmick. Sela is used very poorly. The first episode felt like pure padding until Spock shows up to say "Hi". Like that episode of The Brady Bunch where they say "Davy Jones" 5000 times, we all know he's going to show up at the end.
And despite all that, had this season 2 episode been made (how much of an impact did that writers' strike ultimately have, wow), would drafts for "Unification" eventually appear with people wishing for that instead. (Or why not have both, TNG is a great show but to make it even more Spocktacular...

)