How can one prove that as it may have been intentional and meant to hold something else in place above it?
Darn right. Unless of course the positioning suggested the redundant mortise was positioned over one of the tenons maybe.
Incidentally, on the subject of flexing, in order to fix the lintol circle satisfactorily you have to deliver all the tenons in a perfect, horizontal, correctly spaced circle by means of dropping 40 ton uprights into holes of just the right depth and then wriggling them about. Who the hell could do that? I think we have to be talking The Mekon here....