Hi
First, I've never seen an Honeywell thermostat that was special and didn't fit any HVAC unit. They are all standard stuff.
Second, on the stages and zones, you need to realize the connections are not just "standard" where every installer will do it the same, and it will be what YOU want. Its NOT just connect stage 1 from thermostat to stage 1 of controller, etc. A zone controller CAN base the stage on the number of thermostats calling. For example, maybe if one zone is calling for AC then the zone controller uses stage one. If two thermostats need AC, then the zone controller uses stage 2 AC. In this case, the thermostat zone 2 has nothing whatsoever to do with the zone 2 of the AC. How could one thermostat KNOW how hot it is in another part of your house? It can't. A zone controller can also switch stages based on a timer.
Some of this takes some trial and error and its what YOU want. The installer will be long gone so he probably doesn't care much how it works. I would highly recommend that you read the manual for the zone controller, learn what it can do, and set it the way YOU want. There is NOT a standard way of doing this. ONE stage thermostats can work fine with a 3 stage HVAC unit if its set up correectly, because the zone controller has the smarts. The OmniStat2 is pretty smart but it has NO idea what is happening at another OmniStat2, but the zone controller DOES.
I happen to live in an area with many houses over 10,000 sq. ft. yet the HVAC guys from the area had little knowledge of how a zone controller actually works. Zone controllers are NOT that complex, and if an installer doesn't know if a OmniStat2 will work with it, this also tells me he knows very little about zone controllers in general. Yours might be the first one they have installed.