It boils down to dollars. Right now the Navy has nothing invested in you. You also aren't on Active Duty, which also normally incurs a responsibility by the government to care for you. So if you have something Naval Medicine doesn't like, they can tell you no right off the bat and not lose anything. Once you're on AD, and even more so, once you've started flight school, the military has started to invest money in you, so it's in the military's best interest to work within the system and grant waivers.
You are arguing. And trust me, I've been in the same position and got the same answer (albeit for a different diagnosed..but BS...condition). At the end of the day, an applicant =/= someone already accepted and in the program (or already winged).
Edited: holy typos.