Such a silly work around. I wish stardock or IC or whoever is responsible for handling this part of the process would allow you to start either game without this mess. Seeing as its 'easy' for someone to manually do it, why can't it just be the default?
The reason is because it is a BETA. The final game will allow you to enable Entrenchment if wanted, or play vanilla Sins. And a game will disable Entrenchment if a player lacks it. I'm not 100% sure if you can disable it if all players have it, but assume you can. But that functionaity is a way away. So until they tell you it isn't a BETA, you can't ask for it as they are working on more fundamental things.
Entrenchment should be added as a mod imo, taking up twice the hd space so you can run both isnt logical.
Except that Entrenchment changes some basic fundamental things, so that doesn't quite work. The final version should be such that they are fully compatable.