AnotherGame is a mod for ToE 3.1.

I'm saying it again, the concept of "balance" is broader than you think. For example, you can lower some alt-upgrades to an unacceptably low level, and no one will choose them, but the "balance" in your sense won't suffer, because the faction as a whole will maintain its overall performance statistics due to other upgrades. Balance is also about equal choice, which you won't have (converting dwellings will happen almost automatically).

Yes, of course... :confused:
I've already given an example where one player gets non-native dwellings, while another gets native ones on free land belonging to their opponent (for example, out of 4 possible dwellings, only 2 are available, so there's almost a freebie). Where's the balance in that? At least that...
As for upgrades, this won't really affect things, as the second branch will serve as a reserve, which won't be used much, except perhaps for the Elves with their nimble units...