Potentially destroying whatever balance the modder might have been aiming for with this feature.
Basically, why implement and play with a feature and then make said feature irrelevant?
I imagine one can try to balance for both regaining countries and purchaces being tied to countries, but such a mod would be quite different from anything we have today, and need a considerable amount of design to pull it off well.
But that's not a coherent argument. You're claiming that a feature - which would have to be specifically included in a mod - is dangerous to implement
because the mod would have to be balanced around it.
That's true for pretty much any feature that's included. That alone doesn't make a feature "fraught with danger".
The only way this could "break" existing mods ("because most mods don't include countries rejoining XCOM", according to you)
would be to actually add this to an existing mod without taking into account what the feature does. Yeah, and if I give the basic rifle 500 hitpower it's probably also going to "break" the mod, or if I add elerium as a fuel to the players starting craft. Or if I lock important reasearch behind items that the player can't obtain. I don't see how this inherently any more "fraught with danger" that any other modification, let alone what that should be an argument for.
Regaining countries also doesn't make the feature "irrelevant". What are you even going on about here?