Going into communal changing rooms and showers is in most cases a matter of choice - swimming pools, gyms, clothes shops etc. Transitioning people have the option of avoiding these until the process is complete.

Prisons are indeed a more complex issue, and the authorities are still 'playing safe' by going with the sex assigned at birth in many cases. I don't have a solution for that that doesn't involve keeping all prisoners in solitary for their entire sentence.