I think being able to specifyy some options would be great as well. But, you would really have to get pretty detailed in what options you provided to actually show the *REAL* profit and almost too many variables to really get a true picture. Thus, you'd need a good bookkeeper or accountant (which you should have anyways).
If OSCommerce had/had contributions that focused more on the accounting aspects, then ok, but I'm not so sure that the margin report is the best place to house that information.