4 tons for 1662 sq ft is a lot.
minisplits can be very efficient
but...
if you already having the folks on site
to put the geo loops in is most of the
cost, I'd think adding to install wouldn't
double the cost for the second floor system.

just my thoughts, geo is very expensive to
install in my part of the country. most
go high efficiency heat pump or gas furnace
with high eff a/c.
in other areas of the country geo is less
expensive to install.
what area are you building in?

did anyone do a load calc on the house to determine
the size needed?
also if you build with efficiency in mind, you can
reduce size of hvac with a tighter building envelope.

best of luck.

I don't disagree with energy_rater in any way. You will have to get proposals and analyze the numbers. I will comment on the minisplit operation

I am liking my Mitsubishi minisplits. No leaky ducts and inherent zoning is saving me a bundle. They throttle to a fraction of maximum capacity very well so heating one room with a 4-ton outdoor unit will work very well. They don't have heat strip backup, though other brands do. I have three outdoor units and 7 inside so only part of my "system" will be in defrost at any particular time. I have 11 months with mine now and have not noticed when it is defrosting yet. I live near the South Gulf coast so it does not get very cold here.

I don't know where you get the smaller room stuff. You can get indoor units exceeding 30,000 btu. There are a wide variety of indoor units to choose from including the most common high wall-mounted, floor placement, ceiling-mounted and units designed for short duct runs.

The only drawback I have seen so far is that when the high mounted units approach set heating temp, the blower throttles back and they become better ceiling heaters than room heaters. Manually setting the blower to a higher seed or using a ceiling fan fixes this easily.

What they might not work well for is conditioning a bathroom. For that you might need one of the short ducted units to handle one room and a bathroom. Unfortunately, that will add a lot of cost.

I have found the remote controls of the Mitsubishi not very flexible. You can set on and off times, but you can not really make true setbacks. I will be checking into their hard-wired controls. I would like to set back the bedroom and have it warm when my feet hit the floor in the morning!

OK, I notice the defrost now. It is not a big deal, but it does not get that cold here.

multi zone mini splits bad idea, Mini splits in general are a pain to work on and parts are hard to get also they are very temperamental. Do not buy.... Contractor sounds like he is going easy route to me. I'm sure some will disagree but this is just my experience.