XMN airport was designed as a domestic airport, so they have no good way of keeping those in transit airside. Also the Int. departures don't run all day so they only open up the terminal a few hours before flights depart (at least that's what they did last year).
You just fill out a card on the flight and they check you against a transit list (but they seem to have problems reading the Roman alphabet). It just takes a while.

The flights were perfectly fine, inedible food on most of the legs... but that's not a big factor. My flights were also pretty full, and that's never a lot of fun in economy.