Some white people are scared of black people, should we racially segregate bathrooms? Some people are intimidated by anyone taller than them, should bathrooms be height separated? A lot of people are awkward or uncomfortable around amputees, should they have to use a different bathroom too?
If you don’t want anyone to be uncomfortable either all bathrooms would need to be unisex single-stall bathrooms, or people would need to get over themselves and realize that it doesn’t matter who else is in the bathroom. Until the “bathroom laws” are trying for one of those two things, they are and always will be trans-phobic.