So the concern is a hypothetical scenario where a school implements the guidance, fully supporting trans girls using the female facilities, and at the same time, they absolutely refuse to consider any accommodation to other girls who are not comfortable showering with trans girls?
That would indeed be pretty unreasonable, and I would probably join your protest. I strongly doubt this is, or will be, a common scenario. It reminds me a little of the objection to gay marriage that clergy will be forced to perform gay marriage ceremonies against their will.
On the other hand, being forced to get naked in front of your peers is a time-honored rite of passage for American high school students (and sometimes junior high). In a classic episode of Freaks and Geeks, Sam and the other geeks try everything to get out of showering after PE class, but eventually have to do it. Of course jocks take Sam's towel and push him into the hallway.
Hilarity ensues. Without mandatory showering, this kind of character-building would never happen.