Maybe it's just because I've got gestalts stuck in my cache... But, the gestaltHardwareAttr gestalt can return a gestaltHasSoftPowerOff value. It's possible the Finder is doing a gestalt check to see if soft poweroff exists and not toggling VIA2 PB2 if it doesn't believe that functionality is available.

Seeing as how I now have gestalt altering code, I can see if changing this prevents a soft power off machine from powering off on shutdown.