If the school is more liberal than not, I don't think it would be a problem to talk about your transition, provided that it is related to the application. I know that transition is likely a huge part of your life, and you have probably looked deep inside you for a long and hard. However, when the question is something like: how are your leadership skills and how have you demonstrated them, your transition story will likely not help you too much. If they are asking you to write an essay about a life changing event, and how it has changed you, that might be a better place to talk about your transition. In a field that is more technical like accounting, putting your soft skills down is often a hard call.
Anyway, just thought I'd throw my opinion in, I've thought about it when I apply to jobs too. In the end, it is completely up to you as to the image that you want to present yourself in.