I don't understand this. From what I understand, HVAC sizing is based on the volume of the building. Ducts are placed to deal with the heat loss of windows, but I've never heard of increasing the size of a unit by how many windows you have.
The HVAC Contractor should have been consulted before construction started. He will size the unit and create a plan for the ducting, along with electrical requirements before anything was framed. Then when the house is sealed in, he shows up and installs everything after the electrical is roughed in, and before the sheetrock happens.
In my opinion, it's better to go with a unit that is slightly undersized, so it runs longer, then a bigger unit, that is always turning on all the time. Kind of like a car. You use less fuel when driving at a constant speed than you do when accelerating from a stop.