This is school dependent. Some will; some won’t.
Med schools are not required to allow substitutions. In fact policies at some med schools specifically prohibit coursework substitutions.
The bigger issue is that medical schools are not required to do (and most do not do) transcript audits to determine if admission requirements have been met until AFTER final, post-graduation transcripts have been received as part of the on-boarding process.
Med schools are required to have on record a final official transcript showing all pre-reqs have been fulfilled PRIOR to the first day of orientation. Unless that official transcript has been received, LCME requires that any offers of admission must be withdrawn. With schools holding orientation as early as late June, there isn’t time to take a missing pre-req in the summer prior to matriculation.