This may or may not pertain to the OP's trip, but just to clarify, AGR does allow central-eastern-central sometimes. We did that as a 2-zone award on our trip, but it was the only allowable (published) routing between our departure station (ATN) and destination station (CHI). (Well, the Cardinal routing was also allowed on the days it runs, but that's still central-eastern-central.)
As to the OP's question of how many zones it would be, extrapolating from my experience, theirs should be a 3-zone award (western-central-eastern-central).
AGR let us travel ATN(AL)-WAS-CHI on a 2-zone award, and then CHI-CVS-ATN on the return as another 2-zone award. So, they charged for both zones, but not for re-entering a zone. Of course, we all know it can sometimes depend on which agent you get. However, when I phoned on two other days (re adding a passenger, then inquiring about guaranteed connections), the other agents made no mention of its being a strange or disallowed booking. Therefore, I don't think it was anything iffy.
The 1-zone routing of ATN-NOL-CHI was not a published route, presumably because an overnight in NOL is required. So the central-eastern-central routing was the only (published) way to get there from here. I don't know if that made a difference. It was my understanding that if a routing is a published one without using the Multi-city feature, AGR will allow it.