Private schools usually have their tests on different days (at least they did in Okinawa, where I worked), so I assume Kaisei is actually a public school.
From what I understand, going to the nurse's office does count as attendance, but it would be marked on their record, so it can still count against them. The bigger issue might actually be that Nitori has gender identity disorder. They're not meant to discriminate, but it could be that the school simply didn't want to deal with that.
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