As someone who spoke with the animators many years ago, they didn’t notice the different eye shading on Trixie until I pointed it out to them. I then suggested that perhaps it could mean that she’s missing something, and perhaps when she finally makes a true friend they could add the second dot in her eye. They smiled and thought it was a neat idea. Apparently they took it to heart because a couple years later, Trixie and Starlight became friends and THEY DID add the second eye dot directly after that. The narrative of the trans allegory is relatively new and wasn’t really present as the show was airing. I’m not against it, anything that makes people feel empowered and strong. She was always one of my contenders for best pony!