I agree with all that has been said, density etc of building does indeed affect the price by a big margin!
However, sq footage pricing, along with accurate unit counts does have a place once the building exceeds 50,000 sq ft.
The real trick is to settle on a very tight specification, or else you could quite easily lose your shirt, sq ft pricing is the easiest method of bidding by far, but, you do need to know exactly what you are doing, as contracts this sort of size, have allsorts of penaltlies attached for non performance etc.
Regards,
Rob