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.

I am not sure what $5k covers and will ask. He did give me a separate quote to upgrade to variable speed option.

Upgrade to variable speed Heaters (per unit) - $1,650.00

should I just upgrade everything after the house has been lived in and used?

"We are building a house in east coast."

That tells us nothing. East cost of Florida? North Carolina? New Jersey? Maine? All very different climates and considerations.

I would get the exact specs (model numbers) so you can look at exactly what you’re getting. I opted for three zones from the outset because it wasn’t originally included; the zoning came with a hefty price tag, but it was still less than what you are being quoted for just one additional zone. I think the upgrade to variable speed (or at least 2-stage) is worthwhile when zoning; I’d check to see if the currently planned unit is single stage. I’d also want a higher SEER rating than the federal minimum since that could be raised (and has been in some states).