Well, presumably Mark's calculations assume he's using ethernet, but since he's using hyperterminal(a windows specific clue Mark's likely to have missed) he's probably copying drive to drive. Which would mean the transfer time would be limited by the empeg's bus. Of course, Mark probably could estimate the speed of the empeg's IDE better than most everyone here.
As to why one assumes 5Mb per seccond, 10bT refers to the wire speed, and every protocol on top of that adds some overhead. (each ethernet frame has a header with the mac addresses of the sender and destination, each IP packet contains quite a bit of header information, and so on...)
Matthew