The only way I can see to give a square foot price to the GC would be to do a take off from the prints to get your price then come up with the square foot price based on that.
Then the GC would have his square foot price for each home that was identical to the prints. Anything not on the prints would be an extra. The square foot price would only apply to this exact model of home built in the same subdivision. A different subdivision may require an adjustment to the square foot price depending on it's location.
If the GC wants a square foot price for an additional model of home he builds then you would need to do another take off from the prints for this model, get your price and then convert it to a square foot price. You would need to do this for each model of home the GC is building.
I believe a lot of GCs that are building tract homes have a few basic models to choose from and make modifications to them at the customer's request. If you did a take off for each model the GC offers and came up with a price you could then give him a square foot price based on the prints for each model. You would just need to make sure it was clear that any deviation or changes from what is on the print would be an extra and is not included in the square foot price.
I don't do this type of work so I really don't know but this is the only way I could see giving a square foot price. I can't see giving a GC a blanket square foot price that covers all the different models of homes he builds.
You may want to look into an estimating program such as this one.
http://www.turbobid.net/TurboBidHome.htmlIt works well for this.
An EC in my area does homes for $2.50 per sq ft then he finds people who will come wire them for him for cash under the table. This way he can wire a lot of homes with very few employees. Until he gets caught. He wanted to know if I would wire some for him for $25 per hour cash under the table.
That't the type of thing you'll be up against. Good luck.