to answer your question, the difference may be in the numbers you vs the contractors used for the software. wall construction, duct leakage, window size/awnings etc all affect the load. shade, roof design, also the web numbers may not precisely relate to your design condition.
As far as efficiency loss from outside air goes, it is pretty minimal. If you view it as a concer, then you should have the nit installed single pipe so that you are pulling combustion air from the conditioned space. (you must have adequate free area to pull from)