Emperor God: a god who acts like an emperor, conquering other nations.
God Emperor: an emperor (allegedly) with divine powers, or an emperor who is seen/worshipped as a god by his people.
I hope I didn't give the impression that this was 'big deal'; it's extremely minor. I've only been commenting because I tend to be overly analytical and long winded.
Specifically, I feel that a native English speaker would not be likely to say "God Emperor". If they were reading that phrase, and bothered to think about it, they may likely come to the conclusion you stated.
If you say:
"Cain is an emperor god", the base sentence is: 'Cain is a god'. In this case, 'emperor' becomes a modifier answering 'what type of god is he'. You could substitute any descriptor word instead of 'emperor': 'he is a bicycle god' 'he is a geek god'.
If you say "Cain is a god emperor", the base sentence is 'Cain is an emperor'. 'god' becomes an answer to 'what type of emperor is he'.
Because 'god' is generally a more potent office than emperor, it would likely be considered his primary attribute. If someone read 'he is a god emperor', it's more likely to sound like 'he's really just an emperor, but he calls himself a god too'. If we thought that, we would likely just omit 'god' from his description altogether.
I'm reminded of a line from the movie 'The 13th Warrior' where two 'civilized' men are walking into a run-down barbarian camp. One asks the other "what do you suppose the leader of this camp calls himself?" The reply is "oh, 'emperor' at the very least."
Readers would know what you mean either way, especially in a fantasy game where it's expected that things will be 'exotic'.