Update: Nope, they are not blocked. All commander abilities can be added for the player and then executed. Even cross-army.
I don't know if that was changed in an update and then removed again, but I just tried it and it still doesn't work.
On a related note, is there a way to remove an ability? I'd like to add an ability, have it targeted at a pre-determined location, and then remove it again. I tried simply not giving the player the ability in the first place and just have the script force its use, but that just throws an error about the player not having that ability.