I would think so...not really my area though.
It's just a hunch because I can't think of any other reason why my app would be terminated by the system for using iCloud entitlements when signed with my developer iD, and this app would not be. Maybe some hocus pocus...if the app is signed from the same developer...with the same bundle id as one on the MAS, they just let it go through?
Maybe it's undocumented but an intentional way to say "hey you can get an iCloud container outside MAS but you have to at least have a version of the app also inside MAS." Or maybe whatever checking the system does, is simply not good enough and this is some sort of bug. Or maybe Apple has a really good relationship with this developer.