pdp at the very least I would add damper control for supply air between first floor, second floor and basement. I would look at an 80K 95+% eff furnace that would include the new full modulating furnaces like York/Luxaire and Carrier/Bryant Infinity systems. It appears you have a four ton AC condenser which on the surface sounds oversized. I would discuss with quoting dealers. Any hot/cold spots in your home should be pointed out to dealer for possible improvement. Do you have adequate return in your home's ductwork? Do you have a pleated media cabinet? if not, I would add one. IMO

There are a lot of issues here and a properly done zoned system is not necessarily cheaper - there are a lot of variables. If you use a better staged system (which you would really have to do to make it acceptable), the efficiency would probably be higher. Think of it this way, $4000 per unit or $7000 for an efficient, staged larger unit. Maintenance is 50%. Advantage single unit. If you have NG, and the single unit is in the basement, it will likely be a 90%. If the second unit is in the attic, it will likely be a 80%. Advantage single unit. Conventional practice in the SE is 1 unit in basement/crawl and upstairs unit in attic. If you do a single unit, it would be in the basement. Advantage single unit (since the attic has far greater temp swings). The advantage here is on efficiency and life of the unit. Even the refrigerant runs are shorter to the basement - more efficient. Single unit outside - better use of outdoor space. Advantage single unit. I definitely don't think the answer is always 2 units are better than one. If you can be in the spec homes and try out their zoned system and it is acceptable to you (or unnoticeable), then why not? But you really want to find days that need HVAC a lot and there aren't that many in our future. But you could go and play with the stats and force it to run hard. You definitely should have stats on both floors.

I don't understand the concept of why the low stage can't be used in a dual fuel situation. Let's say is 20 degrees outside and it is more efficient to heat with the gas furnace than the heat pump. The Infinity furnace will use its low stage to try the maintain the set point in the house. It is going to cycle on and off to try to maintain the house at 70 degrees. This is what it does in my house. The Carrier Infinity 58MVB060 has two stages and cost about $200 less than than the three stage 58MVC060. However the 58MVB has a high and low stage, and no middle stage. So in effect you still have a furnace with a low stage. I am not an expert when it comes to installing in an attic. I would be worried about condensation freezing. All I can suggest is you voice the concern to the contractor and have him explain to you how he will deal with it. I suppose he could use an electric heat strip to keep the condensate drain warm, but again I assume he knows what he is doing.

Thats another issue, there is no returns in those rooms, in fact there is only one return in the whole house in the main hallway. It does the trick for the kitchen and living room as that is all in the same open area, and the third bedroom is right near the return. In these old houses I think they assumed the return air would seep out the doors somehow.