Actually, hormones aren't strictly relevant to the calorie calculations - they're just assuming that women have a higher body fat percentage then men (generally true), and therefore have lower daily calorie burns. A cis man and a cis woman of the same weight, activity levels and bf% will have the same calorie burns. (See the Katch-McCardle calculations, for example; it's one of the more accurate calculations and it doesn't take gender into account at all.)

I'm all for the option to add nonbinary as an option, but until that happens, if you'd prefer male pronouns over female, you can just switch your gender and custom adjust your calorie goal. Just select my home, goals, and use custom settings. Personally I still lose eating more than what MFP assumes I would need to eat if I were female, and that's what my hormones are closest to.