What exactly would be "ideal" about separating the bands by zone? Factually speaking, there is no valid reason to do so, regardless of whether it sounds like a good idea on paper.
Easier said than done. For starters, VHF spectrum is at a premium, whereas the state already has countless 800 MHz frequencies licensed, making it a much smoother process obtaining spectrum for an 800 MHz site. You just don't throw up 5-6 VHF sites like that, there is a lot to take into account with regard to the increased propagation (tougher to control the counters of a site) vs 800, diminished in-building penetration in urban areas, and so on. Not all agencies have the capability to operate on both VHF and 800, so the need for overlap is a necessary evil in some areas.
The people who designed and built this system know what they're doing, believe it or not.
Although they are exceeding the original design of the system by adding sites here and there, there are still only a fraction of the sites the OpenSky system needed, and they managed to essentially build this P25 system out on schedule and much closer to budget than could've been dreamed of with the other system. There's no such thing as a perfect system, but they did a commendable job with this one.