It is hard to say how difficult it would be without seeing the installation. I assume the return duct work would have to be reconfigured.

Is the furnace near a wall? I don't understand why it would cost so much unless he had to move the furnace in order to get the larger duct work to fit. Have the contractor explain to you the reason for his price.

Both prices are high. You could get a less expensive media cabinet like Honeywell 200. Installed at time of furnace should not exceed $500. Now is the time, not later which will cost you more.

Talk to your dealer. What model cabinet was he quoting?

IMO

He was quoting a LENNOX HCC20-28 HIGH CAPACITY AIRCLEANER; there is plenty of room to put the furnace where he likes. I don't understand the issue in making sure it will be easy to install later. But I found Permanent Washable Furnace Filters & Air Conditioner Filters, so may stick with the 1" and just use these.