Actually it's not because of when potential ALTs graduate. They are quite happy for ALTs to wait 6 months after graduation before they start on JET [ask anyone from the antipodes]. JET isn't actually about the ALTs, it's about the COs.
The start of a new school year is an incredibly busy time for all staff, teaching and non-teaching alike. They are planning curriculum, sorting out budgets, organising room spaces, getting to know pupils, moving desks, welcoming new [real] teaching staff etc. etc. etc.
ALT supervisors simply would not have the time to properly welcome an ALT and show them the ropes as well as all the other shit they have to do at the start of the year. Even in Australia I always requested my AJT [assistant Japanese teacher] start at the beginning of 2nd term or beginning of 3rd term [second semester] to make my life easier!