Everyone was 16 in their freshman year in this reality. I mean, why not? It's not a documentary. It's fiction. If the creators wanted everyone to start kindergarten at 7 and thus be 16 their freshman year, why not? (And I seem to recall an interview in which either Al or Miles admitted that they didn't know that freshmen weren't 16).

Then a time warp hit Smallville and kept everyone from aging for three years. So Clark was 16 for Seasons 1, 2, and 3, and then the time warp ended and he went on to be 17 just in time for Season 4.