For example at NY med schools, they will have a lot of applicants who took physics at some of the colleges and universities in New York. If you have a weak record in the sciences at Duke, taking a course away from Duke may be read as an effort to avoid science courses at Duke. If you do well, it is unlikely to matter much to them whether you took the course away from Duke. They will have the transcript from the school at which you took the course and evaluate by its own number and their experience with students who took that course rather than by the Duke equivalency number. College is full of trade offs.
Students often make decisions that in turn force other decisions.
For example, the most common reason for taking physics away from Duke is so that a student can go abroad or to Beaufort. Medical schools recognize this fact. Acceptable answers include freeing up your schedule to do something like going abroad or taking courses you really want to take from specific professors that are only taught at particular times, etc. The most common reason for electing to take away from Duke a course that is offered during the summer is financial and I think schools understand that as a reason. The bottom line is that it is not likely to be important to a med school that you take the physics equivalency exam.