I think that the marks made by the beams would have generally reflected the size and positioning of the heat exchanger.
I understand what you are saying -- that the beams could have acted like a pedestal upon which the heat exchanger would have sat and which it would have overhung on all sides -- but this is a weak argument. It is an argument designed to allow you to claim that almost any pattern of marks on the floor are evidence of a heat exchanger.
So no, the marks do not logically eliminate the possibility that a heat exchanger was there, they are not particularly consistent with it either. My main concern is that you then take this weak evidence and turn it into the assertion that "The mezzanine had all the markings for what used to be a heat exchanger." It didn't.
You make your assumptions. I make mine.