There are a couple of factors. (We just sold a house and are about to build).
For one builder we talked to the base price for a specific house to be built on our lot is about $176,000. However, the actual quote for options/upgrades is about $280,000. Now, some of that is to add additional square footage. However, here are some actual prices for upgrades that would be added even if the 2 houses were identical in floor plan.
Converting standard tub/shower to handicap accessible shower only - $1738
Door from Master Bedroom to Porch - $485
Raising ceiling from 8 ft to 9 ft in 3 rooms - $1680
Adding handheld showerheads to 2 showers - $620
Upgrading faucets and hardware throughout house - $1027
Silestone counters in the kitchen in lieu of formica - $8604
Prep sink in island - $908
Adding cabinets and fiberglass sink to utility room - $834
Upgrading windows - $4364
8 can lights in lieu of regular lights - $600
Stone instead of brick exterior - $6600
Upgrading several rooms wood flooring (in place of tile/carpet) - $13,366
Cherry cabinets in kitchen/maple in rest of house instead of standard - $6004
Upgrading roof shingles - $2456
Bronze shower enclosure - $235
Granite counters in master bath - $1500
Undermount sinks in master bath - $500
Wood framed mirrors - $360
Crown molding - $2028
Ceilings painted different color from walls - $1870
I could go on and go. Some differences between similar houses are important functionally. 2x6 rather than 2x4. Better windows. Better roof shingles. More insulation. For some of this you will pay for the added by lower utility bills. Others you won't.
Then there are things that are somewhat functional but also aesthetic. Big ones are things like kitchen counters (Silestone or granite instead of formica). Kitchen cabinets come in a wide range of cost.
Or appliances. There is a huge difference between different appliances. A basic electric cooktop versus a professional range. Or your basic refrigerator versus a $6000 built in very large refrigerator and lots in between.
Lighting. Again, a lot of variation.
Flooring. Some houses have as standard builder's grade carpet and vinyl in the wet areas. Contrast that with ceramic tile in a diagonal (more expensive than non-diagonal) pattern coupled with wide plank, hand scraped wood.
Paint. Like everything else, there is a variation in different quality of paint. Some builders charge more for every room that is painted a different color.
Wide baseboards, tall doors, solid wood doors, wood framed mirrors, crown molding -- It all adds cost.
I could really go on and on. There is just a lot of difference in how you can build two houses of the same size.
We are currently working on house design for the house we are building and are having to make these choices at every turn. Yes, we do want Silestone in the kitchen. No, we won't upgrade the hardware in the secondary baths. Yes, we do want wood in these rooms. No the utility room tile doesn't have to be laid diagonally. We will pay the $4000 to upgrade to the Andersen Series 100 windows, but no we won't pay the extra $6000 to upgrade to the Series 400. Yes, we want raised panel cherry cabs in the kitchen, but flat panel maple is fine everywhere else. No we won't pay to change the ceiling texture and to have different color rooms (but we are still thinking about the white ceilings)...