Depending on the manufacturer of the furnae, it does make a big difference. Most manu. are looking for the resistance of the intake air pipe to match the flue side. If you look at carrier for ex. they state take the longer length of the 2 to determine flue size.
Also the biggest reason is for termination. in a two pipe system it is stated that you can be 1 foot away from a window or door. A one pipe system it HAS to be 4 feet away from window or door. this is to prevent funace pulling a vacuum on a mech room with insufficient combustion air. If a door or window were to be opened in the mech room it would then pull in flue gasses.