Ellen,
I brought a nickle to the table to throw in my two cents, hoping to have some change left over but this is actually a dollar question and I am afraid I don't have enough.
But, in hopes to NOT confuse you with any other shop.

As a general rule I add between 12-18% of the job once I bid it out to allow for an Old world/distressed finish.
Stain jobs only account for about 7-8 % of the cost. While a painted set may run around 5-6 %. For whatever it's worth. I don't bid to compete against other companies. I bid for the opportunity to provide a valued service to go along with our fine cabinets.
You can set up a material such as 3/4\" Birch OW and apply a markup to adjust for this in the system. If your customers wanted to upgrade to an Old world/distressed finish, simply change the materials and then do a cost analysis for the job.
For the most part of costing out a job I place a $ on the larger more costly to build units such as a bank of drawers, refrigerator, or a oven units. I then do a lineal/foot bid for standard base and uppers, then I add the unit cost. Then I add a % up charge for the finishes.
I really hope this doesn't get you confused. My intent is to help add to you knowledge.