The number and height of the pins isn't the only difference.
There's a thicker o-ring included with the GT which makes the base bow like on the FuZion. Tests done so far indicate that a bowed base yields lower temps than a flat.
The thicker o-ring wasn't included with the early GTs. Contact Swiftech and they'll send one for free.
EDIT: Virtualrain over at XS compiled a list of all FuZion tests,
link. FreeCableGuys test includes both Apogee and Apogee GT.