Yes, install a separate zoning control for the basement. Now is the time. Yes, I think both furnaces are oversized. Makes me wonder if he sized the furnaces not for the heating BTU capacity but for the 4 ton rated blower that would be needed for the 3 1/2 ton condenser. Yes, based on heat gain calc, a three ton condenser seems to be right size, not 3 1/2 ton as quoted. This should be questioned. Keep in mind, 36 KBTUs=3 tons. I would want to know the design temperatures used both inside temp and outside temp both for winter heating and summer cooling. You want excellent ductwork insulation for attic. That's a long way to blow air. You might consider an 80% furnace for second floor installed in attic. This would eliminate the long distance or perhaps insulate attic where it can take a high efficient condensing furnace without fear of freeze ups. The 80% would be a less expensive option. Discuss the options with dealer/GC. Nothing is easy is it? IMO

It's not that hard with the software. Basically, you feed it the square footage of each room, the type of insulation in outside walls and size/type of windows. You tell it what temperatures you want for winter and summer and what the averages are for your region. It sits and thinks and spits out numbers, usually in BTUs for heating and cooling. From that you get your tonnage for cooling and BTUs for heating. BTW: I might be asking for a bit more insulation in the attic if this is new construction. R-38 would be a little light for me. I might be looking for R-50 in Penn.

Now that you have discovered you have natural gas, are you going to investigate who much it will cost to bring a pipe into your house? I don't see in the load calculation the R values for the walls and attic? Do you know what values were used for spray foam and batt insulation? Do you know how the spray insulation will be installed in the attic? Will it be open or closed cell? The firs quote is for a 4 ton single stage heat pump (XR15) while the second is for a 5 ton variable speed heat pump (XV20i) which is Trane's top of the line product. It is not a fair apples to apples comparison, but the price gap is big. You need to ask about the size for the second quote.

An unconditioned attic is the worst place to install HVAC equipment and duct work. I would avoid it if possible. If you are in DC or one of the bordering states then 14 SEER is the minimum allowed. For a walkout basement having a separate zone is a nice feature for heating, you probably don't need it for cooling. The $5K price is steep for a thermostat and some dampers. Do you know the model numbers of the HVAC equipment. At the very least you should have 2-stage equipment if you are going to add zoning. Find out if the $5K covers upgrading the equipment for the first floor.