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.
The TRUE highest cost system is the system not installed properly...
Find a HVAC-Talk Contractor by clicking here
Do you go to a boat repairman with a sinking boat, and tell him to put in a bigger motor when he tells you to fix the holes?
I am yourmrfixit