I think a more direct comparison would be flying the US flag with a state flag covering half of it.
Personal identity flags are perfectly fine, alongside the rainbow pride flag or just on their own. Just don’t cover over the “everyone” flag with specific identities. That’s like the opposite of the flag’s meaning.
Connect them together for efficiency, and maybe use both rails for stability and to reduce design conplexity. (you dont even need any additional infrastructure!) Also, have them arrive regularly, so that users don’t need to bother with an app! Brilliant!
Seriously though, it’s really amazing how people keep inventing trains but worse. I guess this idea makes some sense if there aren’t enough riders for regular train service, but still…