It's become pretty clear that the ads that were coming out a few years ago opposing trans people using the bathroom that reflects their genders which depicted men following little girls into the bathroom were mostly conservative propaganda.
Trans people tend to, suprise suprise, transition. They go through years of hormones and often have surgeries to present as the gender they identify with. There are people who I grew up with who have transitioned and, if I hadn't known them for years before transitioning, I would have no idea. In most cases, forcing trans people into other bathrooms would create uncomfortable situations for everybody.
There's a difference in the issue between trans people and gender-fluid people, at least in a lot of cases. If a trans-woman like Blaire White uses girl's room, it wouldn't make sense to have a problem. Most people wouldn't notice. If a person like Alok, who has a full beard most of the time, uses the girl's room, I think that a lot of women would be justifiably uncomfortable.
Realistically, if rape is such a rampant problem on campuses, saying that all a young man needs to do is say that he's gender fluid and wear a skirt (as the young man who was recently arrested for raping a girl in a Virginia school bathroom was), there are a lot of bad people out there who would look at this policy as a golden ticket. I mean, if you don't even need to trim your beard in order to gain access to the girl's facilities, that strikes me as an issue. Since schools are so insistent that the policy needs to work, they're doing their best to take care of the people who abuse the system and bury the people who are being abused.