Depends on what you wish to do lass. It’s fiction, not academic work and I believe the author is free to make his choices. However given that you’re aiming at historical fiction, the historian in me has to tell you that there are things to consider.
An Empress would not have been impossible… during the 5th century maybe. During the second and third centuries it would not be unlikely but impossible as a matter of fact, sparring you all the details on succession during the first phase of the empire, just know that as a matter of fact there wasn’t a fixed law on succession, hence two civil wars that led to dynastic changes in 68-69 and later 193-197 because the imperator didn’t have a designated heir. And this heir always was an aristocratic roman male citizen.
But that’s the thing, I think it would be a strength for the story to explore these potential loopholes. Giving a background story on how the MC came to power would not only be interesting but present us with opportunity in an alternate history story. How and why and she got designated, her background, so on…
Tricky but if done right I believe a gender-locked female game would be very good since the idea is awesome and the opportunities are many. By all means have at it.
Then there is personnal note. As I said, it’s up to the author to organize their work but if you ask me, a genderlocked female story is tricky enough and more importantly interessting enough as it is and I don’t see how you’d make it work with a non-binary MC. If your original idea was about a Female NPC you should go that way, but I don’t see how the former would bring something additionnal to the story. The whole point of the story is to explore the possibility of an empress, if you’re going to add stuff than you should go all the way and do the usual format of “MALE/FEMALE/NON-BINARY” but I feel that would make the experience less original. Genderlocked female games are rare enough and the idea is good so as far as I’m concerned, this format is enough for a good game.
Plus, I don’t like it when people are trying to apply modern concepts to ancient societies which didn’t consider or even have them. You cant reason and imagine an ancient society by today’s thinking and expectations. It’s called anachronism and there’s an awful lot of it going because of the general public. Remeber, by today’s standards roman society was highly inegalitarian, with power held by men and overall very different from what we know from modern societies. The state or service to it however was also an opportunity. There are different dynamics to consider. History and alternate History are rich and complexe enough as they are without having to rewrite mentalities or oversimplify things. Don’t pull an Assassin’s Creed : Odyssey.
Well that being said, I think you have a good thing going on their, good luck wit it.