I think that having a NONE settler unit prevents a civ from being destroyed, so you can place a zero movement high defence settler in a remote part of the map, if you really need a civ to be permanently alive.
This trick seems to only work at the beginning of the game. When the destroyed civilization has 1 or 2 cities. In the mid or late game, it doesn't matter if the civilization has a NON settler. When the last city is captured, it will be destroyed for sure.
In any case, I would recommend that you test this trick more carefully (in the mid-late game stage) if it makes a big difference in your concept before getting to the main work.
I can confirm that the mechanism works perfectly. I simulated the game up to modern times and then conquered two civs with another civ. Then, just to be really sure, I captured every city on the map with the barbarians, all the civs are still in play, and all of their units without a home city. For the simulation I used the normal tech tree and the settler units (NONE) had an edited bonus slot.
Well, I'm glad you're doing great.
I did similar tests about 10 or 15 years ago at MGE. I also used non-moveable NON settlers. In MGE, this trick definitely didn't work. From about the 200th round (mid-18th century), destroyed nations can no longer be reborn. Therefore, with the capture of the last city, the nation inevitably disappeared from the game. No matter how many NON units of any class she had. They just automatically disappeared after the fall of the last city.
Probably TOTPP fixed something in this game mechanic, since everything works fine for you.
I hope I didn't sound like I was discrediting you.
Yes, I also think this solution was not yet possible with MGE. In the "Selected Custom Files" dialog, I also selected the "Don't Restart Eliminated Players" option. Maybe it has something to do with that too.