Okay, we're doing this on General. Seems like a better fit for Open Discussions.
Erick, I appreciate that your thinking is highly nuanced but I want to address the base level of what you are saying. Feel free to correct me if I don't seem to be hearing you correctly.
Sex is anything but deterministic. Whatever the level of rarity of intersex conditions, the fact that they happen at all is proof that sex is not binary in nature. The "reality" of an individual's physical sex is essentially the entire story of how their body developed from the time they were a zygote up through puberty, and beyond. And its none of your business.
And sex has nothing to do with gender. Gender is entirely a social construct, the same as race. if you think you know a person's gender better than they do, that's an act of aggression against their right to live their lives.
Transgender people don't deserve your "charity" they deserve your respect and admiration for being brave enough to be themselves amid casual and generally accepted transphobia.
These points are all essentially moot. Someone may be able to ban transgendered people from practice at their dojo, or force them to use the wrong bathrooms or changing rooms in certain localities today, but that's changing. Eventually we'll get to the point where they have the same rights as cisgendered people and you will be facing lawsuits if you discriminate.
P.S. the idea that a transgendered person cannot be taught Aikido because they cannot understand the proper relationship between In and Yo is not just transphobic, it is sexist. Just so you know!