I won't comment on your hypotheses, but...
Considering they died by our hand, and we died in the Bad Future to Black Rose, both Emet-Selch and Elidibus should still be alive in said Bad Future unless someone else found a time and way to do them in for good.
Minfilia, having been reduced to little more than an errant soul lending power to and occasionally possessing girls / young women, should have been killed (or rather her soul returned to the Source's lifestream) when the First was rejoined as per the Warriors of Darkness' original plan in 3.1 - 3.4.
Hydaelyn would still be around, albeit even weaker than before due to needing yet more energy to maintain her seal on Zodiark.
The latter part is news to me. I'm normally pretty lax about it, but do you have a source?