This makes perfect sense - people saying "WTF, they got the size wrong and now they're changing the name?" have got it all wrong. Apple never called this the SE2 (they haven't mectioned it at all, of course). It was dubbed the "SE2" by some analyst, or (more likely) random website. This phone is a natural successor to the 8 and never had anything to do with the SE, except in hopeful minds of the SE faithful. The only name more appropriate than "9" would be "8S".
I expect that Apple feels there's no worry about the two naming schemes (6/7/8/[9] and 10/11/12) overlapping , because this (the old) line won't go past a "9S" - they'll have fully moved into the 11/12/13/… lineup by that point.