Of course it is mod compatible. But once you mod the game you can't just expect it to always work once you remove that mod and try to play the same saved game...
I don't expect it to always work in every single case, but I expect it to work where modders are technically able to get it working, a la Skyrim, not have a situation where my Santa Hat mod breaks my save file just because "all mods break save files."
It wasn't the case on XCOM:EU, I'd expect it to be the same as or better than EU as a minimum, and from what I've heard about Hidden Potential it's not true, which is incredibly scary.