One of the questions on the Common App is “How long have you known this student and in what context?”
Colleges understand students select teachers they believe will write the strongest recs. What message does it send to admissions if a student appears to think their best letter comes from a senior-year teacher they’ve only had for a few weeks or part of a single semester?
This is also why I feel the OP’s son should ask for a rec from a different teacher in a class he’s already taken. Colleges may very well figure the letter from the Calc teacher is the best the kid thought he could get someone to say about his organization/work habits.