I think the pop system is once again similar to how it was in CivII. In SMAC, every citizen equaled exactly 10,000 population. But in the hostile environment of Alpha Centauri, this made sense because base growth was supposed to difficult in that rough terrain.
In CivIII, I suspect that each citizen's population value will increase throughout the ages, which I believe was also done in CivII.
As far as exactly how the computer resolves this, I couldn't tell ya'.