I am renovating my 4500SF 3 floor house in Cambridge, MA. The house has a flat roof with no attic. I want to finish the basement at some point in the future so I want to minimize duct work in the basement. I had the idea of running two systems(east and west) from the basement, each system with a vertical supply trunk supplying half of a floor. The system will be fully zoned. 3 zones for each system, 1 zone for each floor, total 6 zones. I will use Carrier Infinity zoning with a carrier modulating furnaces and 2 stage condensers.

I have gotten bids from 3 different contractors that I feel confident in. 2 of the installers were OK with 2 systems each supply air to 3 floors. The third installer didn't think it would be a good idea to supply 3 floors with one system, even with each floor being zoned with Infinity. He wants one system to supply the first floor and another system to supply the 2nd and 3rd floor. I don't like the idea of supply and return trunks transversing the length of my basement in that scenario. But if the system would be materially better I guess I will have to live with that. Any thoughts?

ps. The winning bid as part of the contract will perform load analysis and duct calculations, I am insisting the duct system be properly engineered. The house will be fully spray foam insulated.