There is no "automagic" though, things have to be handled, as the game API usually sets to "enemy" as default value for the concerned script call.
There are two things to do with the aliens (called the native life forms in this mod, as used by SMAC):
1/ Forces that will be skipped in the destruction blast of fungal missiles. I know similar mods like this that will create multiple native forces, So I have added mod option "Forces of native life forms". Users have to add the names of all alien forces to it. So this needs a bit manual input.
2/ Forces (faction) of spawners that are created by the fungal missiles. I have to admit that this point is overlooked though... I have not added the force=... property to the line (control.lua line 323 in 0.18.0). So it will create with the default value "enemy".
To add point 2, it would be algorithm-wise and UPS-wise difficult to determine which force (faction) "owns" the territory the fungal detonation occurs. (Searching the area to count entities of various forces can be expensive.)
So my idea is to keep it simple: draw one entry from mod option "Forces of native life forms", all spawners created by one fungal missile will all belongs to one single force. I will see if there are better solutions, before implementing that.
PS: I have not expected it to be used to initiate alien civil wars... But after fixing point 2 in the coming update, nothing stops you to do that. :-D
