I really like the 2nd idea. From my first playthrough I wanted to do some interactions with these characters in any possible way. Sadly nothin worked
but idea to save them sounds great to me. It could be some sort of sub quest if syahata reach shelter (if it would act as a base) and would go on expeditions to various places, including old places where she could help everyone "alive"
This also adds some gameplay to these npcs. (Not saying we gotta save all of them, but maybe 2-5 NPCs to save throughout whole game, each with certain animation / role inside base and so on)
Like this idea much tbh. Though it would be pain to program and animate :<