I don't want to debate genetics, or the morality of transgender issues. I understand it has a genetic basis, but at some point a person who has lived as a man decides to transition. I understand that this aligns her with her own feelings and is a better fit for her, but she also could have decided to remain male and deal with the incongruities.
But your example is odd. Yes, Brianna Stewart has an advantage over others in her sport. That is nothing unusual. Taller players of either gender have an advantage over shorter players in basketball. Heavier and stronger players in football linemen.
What matters is that Stewart has been a female her whole life. Let's examine your equivalency further. Suppose Stewart wanted to compete in the NBA. How successful do you think she'd be? Even Diana Taurasi, with probably the most complete set of skills in the WNBA, never tried to compete with men. Why do you think that is?
Or let's go the other way. Let's take an average NBA player, let's say a 6'11" forward like Harry Giles of the Trailblazers. Suppose all his life he felt like he was really a woman, and decides to transition. Do you think it is fair that he should now be able to compete in the WNBA? Maybe you do, but most women do not.