Your school seems to be a bit ignorant or messed something up. AFAIK you get 3 months on arrival with edu visa then 3 extensions every 3 months resulting in 4 stamps and total 1 year of studying visa. AFAIK even after the year passes some schools can enroll you for next year without you having to leave the country (since few months ago)
The visa stuff always changes here and legality is always in various forms of gray because everyone's lost.