The 4 inch filter is better because it has more surface area. The larger area decreases the resistance to the air flow. The 4 inch cabinet is a three sided box with a door in the front. It should add much cost to the installation. I recommend getting it if can be made to fit.

The 4 inch filters are more expensive, but you should go 6 - 12 months between filter changes. The Filtrete filters are very restrictive.

Virginia

How many returns do you have for basement and main floor?

And just to be clear, the AprilAire mdl 2210 is filter media cabinet that is normally attached to the return side of the furnace.

The up charge to go to a 95% eff Infinity furnace is absolutely absurd. Makes me wonder about this dealer. Have you considered getting another dealer involved in the quoting process?

IMO

Here is a link that might be useful: AprilAire Whole House Media Filter Cabinet