The AIE system is just one layer of security. DOD made the post decal system optional awhile back, too - and now Ft Stewart is supposedly one of the few installations that has decided to keep that system going in addition to AIE and gate guards.
The layer of security the AIE system provides goes like this: the vehicle driver swipes his/her registered card, and the green light means that person is in the system and approved for access to the installation. I believe the system also makes a record of the swipes so there's a record of which registered persons come on and off post. However - as we all know - vehicles sometimes have more ocupants than just a driver. The driver could be a hostage to terrorists, so the gate guard is there to make sure that anybody NOT in the AIE system is screened as well. No record of the passengers is compiled, but I suppose that they figure they can backtrack and gather this info if they have to by contacting the AIE-registered person.
Having the AIE system in cases where driver-only vehicles go on and off post theoretically mininizes the interaction between the gate guards and the individual vehicles, which may enable them to also minimize the number of gate guard JOBS.
My hunch is that the powers-that-be at Fort Stewart decided that this particular post needs several levels of security - to include guards, AIE and a post decal system - to give them an appropriate "handle" on who is coming on and off post. My understanding also is that when security levels are enhanced at Fort Stewart (above ThreatCon Alpha which is the state now), they MAY decide to limit post access to vehicles driven ONLY by people who are registered in the AIE system. As I recall, you get photographed, fingerprinted, background checked (kinda-sorta), and everything but a colonoscopy when you are AIE-registered. So when the security level goes up, they want to strictly control who comes on post and restrict those from the installation who are not in the system.
The Bottom Line: It's just another way that Big Brother can reach out and touch you before, during and after the fact if they want to.