The two first waves are hard coded in the sense that they'll always occur and will generate void dorfs if real ones are not available. If real dorfs are available members of the first two waves tend to be drawn from existing populations.
You can, of course, set up a bunch of fortresses that allow only a small amount of immigration, but it's easier to get reproduction going in a single, larger fortress.
Retired fortresses are partially abstracted, so they'll probably not starve to death even if (non dwaven) caravans were used to keep them alive. Titan attacks are handled in retired fortresses the same way as in game generated ones, using some kind of abstract mechanism, so your careful defenses are useless, while all members being high level military dorfs should help, but numbers are important. However, your first fortress tends to kill off the titans...
If HFS is opened and not plugged properly I assume the fortress will fall. It will not be goblin controlled, however, since that's a world gen thing only.
I don't know if completely closed fortresses would send migrants, but would not be surprised if they do.
I don't know what it takes to revive a civ. Bringing the starting fortress up to metropolis level (almost 80 years), and then reclaiming the mountainhome wasn't enough (but I didn't continue after clearing out the completely water less mountainhome). I've seen it said that building up sufficient fortresses/pops can eventually achieve it, but don't know what it actually takes.
It's actually worse continuing in the same world, since world activation is broken. The civs crumble and die, i.e. their sites remain fully populated, but the civs themselves do not control the "free" sites, and gradually move over to the "struggling" side, with no members left.