"Stryker's" eyes clearly flash yellow - the same as Mystique's in previous films, and even Days of Future Past.
In this interview, Simon Kinberg 100% confirms that it is Mystique impersonating Stryker.
Stryker is a character that keeps reappearing in the franchise, perhaps because he’s one of the only identifiable bad guys the X-Men have encountered. And then, in the final beats of the film, it turns out he’s Mystique — the ultimate “WTF.” Will that payoff in the future?
We really wanted to do something subtle with Stryker in this movie. We wanted it to be the beginning of the origin of him. He’s in the shadows most of this film. In some ways, Stryker was included in order to trigger something for Wolverine. How would it impact Wolverine, going back in time and seeing this guy who is going to manipulate him in the future. That was just interesting. Stryker’s been interesting in the books and the Brian Cox version was fantastic. But the last moment in the movie with the Mystique reveal… there’s for sure more to that. As we follow the characters in to X-Men: Apocalypse, we have to address that and make it a real thing.