Gidday,
I'm glad someone else has noticed this in ETO. I posted some screenies about it years ago (getting NZ flags on the allied side of the frontline, and SCW flags on the Axis side) - wierd stuff like that! I even added #flags to some facilities (eg invasion defences) so I could get a clearer idea of what's going on.
One of the problems with random nationalities is that for some facilities specifying a lot of vehicles, the randomly assigned nation does not have a vehicle for every type - hence you get facilities which are pretty empty and missing spawned components.
My first guess was that my experiments with the country.xml file, where I change the default spawning nations for air spawns and vehicle spawns, also allowed the random nationalities for facility spawns. But maybe it has always been there and no-one has mentioned it?
IIRC in one of the SDKs, it is mentioned that facilites DO spawn with random nationalities for the relevant alliance (I just never believed it was commonplace). It will likely either be the mission and spawn scripting SDK or the Campaign SDK which mentions it.