Sorry I hadn't gotten back to you about this. I think I downloaded your testmap on my desktop PC in my dorm room, but currently I'm on break at my house and the map is no longer available.
I just ran a really simple test; here is what I really think should fix the problem:
1. Don't give the building Descend/(custom Root) in the unit editor, so it won't have the bug between Undead build + root.
2. Add the custom Root ability to the building when it is completed -- just a little trigger "Building finishes construction" type event for the Terminus Crux, that just adds Root.
3. After adding root, call the "Play unit's 'stand' animation" action on the completed building. (Otherwise, another bug is encountered where the Birth animation is played because the building's data is all reset by giving it Root somehow, but it uses a linked model for UBirth that has already finishing its own "Birth", so the building becomes totally invisible.)
Let me know if that method does not work. I really think it should do the trick.