I've never heard, or thought of,
Troy as being anything but very masculine. I've only known one
Troy, handsome and an excellent student and athlete. Despite the sound being similar to
Joy, I can't see
Troy suiting a girl at all.
Troya sounds more feminine. If you hadn't mentioned that it's a legit place name, I'd think it might be made up. It did bring "troika" to mind right away, the nearest association filed in my brain. I can't say I immediately like it, but I think I could get used to it.