IANAL, but I’m pretty sure that this argument doesn’t necessarily apply when it comes to protecting the rights of “a small percentage of the population”.
For example, homosexuals are also a small percentage of the population (though larger than the percentage who are transgender), but the courts have mandated (quite rightly IMO) that the millennia-old “societal norm” of limiting marriage to opposite-sex couples be changed in order to accommodate their right to marry.
Denial of marriage rights to same-sex couples had also been considered “not an issue” until fairly recently. But that doesn’t mean that the denial of rights wasn’t real. Majority rule does not extend to infringing the rights of minorities.
Well, no; that’s like saying that we as a society are, or have been, heterosexual. The fact is that for thousands of years most human societies have adopted a social fiction that everybody is naturally cisgender (according to a binary definition of gender) and heterosexual (and also right-handed), and that individuals who don’t conform to those norms are pathological deviants afflicted by some type of illness, deformity, or just plain evil.
Many societies are now coming around to more scientifically accurate models of sexual orientation and gender identity that recognize a more or less continuous spectrum of tendencies instead of artificially rigid universal norms.
Why are you assuming that a gender-neutral multi-user restroom can’t have urinals as well as stalls? In my college days I lived in a dorm with a gender-neutral multi-user restroom that had a urinal as well as stalls, and I never heard of anybody having a problem with it.