This will be case by case and school by school. If it's not late, it's definitely at the end of on time. I'm not going to do this, but several schools have stated that they will send secondaries, and even extend IIs without a MCAT, although no school is waiving it before making a decision.
Conventional wisdom is to not send an application to a school you care about without a score, but, and only you can answer this, if you are reasonably confident (based on AAMC FLs) that your score will be competitive for the schools you are applying to, you can submit primaries and secondaries without the score, and some schools will be okay with that this year.
End of September might very well be considered late at some schools, even this year. You really need to check with each school you are targeting before making a decision one way or the other. If a school is making an accommodation and is willing to preliminarily review an application without a MCAT, and you don't submit until the end of September, yeah, you'll probably be considered late at that school, since people will have been submitting since mid-July, both with and without scores.
