Good question Craig,
No, it doesn't actually shorten the "throw" of the shifter, as is explained by the description of "removing the extension". However, before the idea of destroyed syncros gets you all excited just be sure you've read all the info:
The shifter handle in the Protege5 is designed for a more comfortable shift, taking in to consideration the design of the whole center console. The length was chosen for it's distance from the center armrest and an equivalent height to that console. The end result made the shifter seem really high, but most "non-sports" minded drivers don't seem to even care much. However, those of us wanting a sportier feel look at it like it's a "school bus" shifter. The extension on the handle was installed to give it the required length to fit the criteria I showed you. Now, look at the MP3, the same console design, but a shorter shift handle. Sportier feel, because it's supposed to be a sportier car. By removing the extension in the P5, you get the equivelent of the MP3. Most of us here are in agreement that the MP3's stock shifter is exactly that: the same parts as the P5, without the extension.
I've had mine off now for about 6 months, and notice no increase in shift effort and have not missed a shift once. So if you're just wanting an improvement over the stock "school-bus" feel, then go for it. If you really want a short shifter, then spend your big money on a B&M or something.
