There's still no correct orientation even with an H-S-H. If you prefer how your pickup sounds with the cable exiting toward the neck you just want to wire it in reverse to keep both inner coils on in positions 2 and 4.
I don't mean right or wrong in terms of sonic nuances. I mean correct way in terms of consistency with the wiring diagrams. If you follow the wiring diagrams provided by Ibanez and DiMarzio you have to flip the neck pickup around to get the standard inner coil splitting. Of course you are right that you could swap the hot and ground on the neck pickup but that's not how the diagrams are drawn and should you ever decide to have one switching alternative that includes neck and bridge in humbucking mode they would be out of phase. I think to keep track of the wiring it's useful to actually stick to the diagrams... and correct pickup orientation to achieve what the diagram suggests. But maybe i am just being german... :-)