Combining the two expansions can end up locking Umbral Choir out of expansion room. Recently I had UC start next to the Academy. Academy systems have pop number but they cannot have Sleepers (I guess it is to avoid the problem with spying on the "fakely populated" system) so there is no way to install Sanctuaries there. I was unfortunate enough to get the Academy expansion line go perpendicular to my way to the center of the galaxy. At the point it happened no empire was strong enough to conquer the Academy systems and resulting hacking paths were so long I was left with nothing to do for tens of turns.

Actually, I don't even know what happens when a Nakalim player tries to donate a system having Sanctuaries to the Academy, is the attempt blocked or the Sactuaries destroyed? The Academy is unable to colonise systems with Sanctuaries so if you see an Academy settlement ship orbiting around an empty system for a long time it means the Choir is already there.

As the "Ideas" section is closed I decided to post here. I'm not sure if it is a bug report because I could move my system to a different special node (what still took like 30 turns) to escape and unlike Pirate League the Academy does not track hacks back so there is no risk involved in doing that, it's just slow. However, I think at least the Choir should be allowed to install Sleepers and get Sanctuaries on Academy systems (an in consequence abduct pop with hacking/conquering the system). I don't think that's moddable anyhow though.