Ha! There could be more than one answer I believe. For one, a manual trans driver needs to have the best balance ergonomically for shifting, and the longer shaft is easier to reach. (Look at some race cars...jeez, their shifter shafts are loooooong!)
Is the throw longer? No clue....normally, you'd think the longer the throw the less compact the shift pattern is on the trans (like in a UUC Short Shift kit). But, not necessarily......I believe it all gets down to a cross between ergonomics and physics. What's comfortable and what gives you the best shift "feel" without compromising comfort?
If you strictly think "physics", doesn't a taller shaft help tighten up the movement of the mechanism at the transmission (due to the application of "leverage")?
Maybe I'm all wet, but those are my thoughts. All I know is the stock manual shifter feels great....look at the diameter of that shaft!
John