The MATS Part 1 will say what it does because its the Manual of Air Traffic Services - therefore written for controllers so its permitting its intended to abbrieviate callsigns. I expect that the Air Pilot will have similar entries permitting abbrieviations from a pilots perspective.
As a controller I will always repeat the callsign in full on my first transmission to ensure that I have the full correct callsign, and thereafter will always use the abbrieviation - subject to any similars obviously.