Well, it makes sense to say that to get a higher pitch (with the same provided sample), you'll need a higher frequency, and to do that you'll have to speed up the 'tempo to get the desired note (for example, D-4 from the initial, C-4) you wish to play. It also applies to notes which are lower than the initial.
Back then, when Karsten created the first tracker, he didn't have the capabilities, or much rather, technology isn't quite catching up well. So 'higher/lower pitch w/ no 'tempo' differential' thingy was not accessible, nor was it understood (I really don't know what other ways to explain to you).
I'm no expert, but that could be one of the many other countless theories out there as to answer that problem.