There's a massive mall near where I live (in a major, metro area) and they have a gender-free bathroom. All folks use the bathroom- the doors go right to the floor and ceiling, but the hand washing is co-ed. And I've never ever heard of anyone getting attacked in that environment. So I find it extremely hard to believe there's any evidence to support it happening on a smaller level involving trans folks.
I think that's the best design for public restrooms. That change is very similar, in my mind, to the change that removed doors to most restrooms in places like airport terminals. They put in curves or turns for privacy so nobody has to open a door to enter or exit.
Where people get rid of waste or need privacy for other reasons would be singular cubicles. WHY are there urinals in public restrooms? Nobody has urinals in apartments or houses. Men can obviously urinate without them.