When someone says "factory short shifter" in the context of a 986 Boxster there are actually at least four different parts they may be referring to.
The picture shows three of them:
1. On left we have the standard 9x7 shift console, a factory Porsche part which reduces the front-to-back and side-to-side throws by about 15% vs the 986 shifter. Note the black plastic middle piece, and steel part that bolts to the side. (This is white plastic on the 9x6 shift console.)
2. At middle in the picture, we have the 997GT3.2 factory shift console (not Tequipment or aftermarket). It has the same geometry (and throw reduction) as the standard 9x7 console, but replaces the "rubbery" feeling, (and prone enough to wear that by about 100k miles, they will almost certainly be "shot") hard plastic+polyurethane bushings with tighter, and longer-lasting solid metal bushings. You won't be able to shift in a straight line diagonally across gates anymore like you can do with the more rubbery plastic+polyurethane bushings, so it feels different.
3. At right in the picture above, we have one of two different "genuine Porsche aftermarket" Tequipment short shifter kits which Porsche has sold aftermarket as replacement "upgrade" part. Note the blue plastic piece, substituting for the black plastic piece of the 9x7 shift console. This provides the exact same side-to-side throw as the 9x7 shifter, but reduces the front-to-rear throw significantly more than the 9x7. It has the same plastic and polyurethane bushings as the factory 9x6 console and standard 9x7 console.
Supposedly Porsche offered at least one other Tequipment aftermarket short shift kit, and the one linked to below seems to be what most inexpensive, generic aftermarket "short shifters" are attempting to copy:
Porsche Short Shifter - PelicanParts.com.

This has more aggressive throw reduction than the 9x7 console, although I'm sure exactly how it compares to the blue plastic tequipment version. I think both of the aftermarket Tequipment consoles are the most aggressive in front-rear throw reduction than any factory (non-aftermarket) options.
Hope the info helps. Best of luck!