I read all the posted chapters of this story and it is really wholesome. I really wish that this was how I were treated by my parents when I came out of the closet.
Akira did have some interesting character growth in that series though. Nanako was just crap for most of it, not until they decided to not go back did she become decent.
Most gender benders unfortunately have the same thing about the former girl feeling like they can do whatever they please...
This debate could easily be solved by distinguishing between Physical Yuri and Psychological Yuri.
Physical = Biological female or a post-op transsexual
Psychological = Female gender identity
So this is physical but not psychological yuri etc.