However, focused on sound as it is, is there a reason why ā in a closed syllable is not transcribed as "o"? E.g. pausal wəqāṭā́ltī as "wəqāṭóltī".
EDIT: Wait a second! You did write pausal qoṭᵊlā́ with "o". Does that mean there is really a stressed long קמץ vowel in the middle of wəqāṭā́ltī there?
So, yes, I meant it the way I wrote it. I'm not careless about these things (although I'm not immune to typos and copy/paste errors, but this is not one of them).
So the best way to avoid confusion regarding the קמץ is to understand that really there are two completely unrelated sounds ("ā" and "o") that happen to be written with the same symbol. There is a reason they share a symbol, because in the Tiberian reading tradition they were the same vowel, though perhaps still differing in length, but it's best to ignore this and think of these two vowels as separate and completely unrelated.
The reason I say this is because it is important to realize that when you are asking yourself whether a particular קצץ is pronounced "ā" or "o", what you're really asking is which of these two unrelated sounds is this קמץ indicating here. The rules about closed and open syllables are guidelines to help differentiate the two sounds, rather rules of how קמץ is pronounced. Now in pausal position (most of the time) a stressed "a" is lengthened to "ā", so even when this happens to be in a closed syllable, it is still "ā" and does not magically become an "o".
The above is just to help you understand things better, because really there is a simple rule here that you can remember instead: a קמץ that carries a primary stress is always "ā". This is because there is also a rule that "o", when stressed, is always lengthened to "ō" (and represented by a חולם).
Side note: qoṭᵊlā́ is not a pausal form.
Is it always -nī (as in Standard Arabic) or is it -nī most of the time?
Yes, always. Did you have a reason to think otherwise?