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In my experience, it is normal practice to factor time into the estimate (call it risk factor if you want) to push your skills. You factor a profit margin into your estimate right?

As long as the customer is satisfied with the overall quality, cost and timeliness of the product, you've met your obligations as a business. Why does the "profit" always have to be only cash? learned skills are a form of capital reinvestment that the customers pay for just like they pay you a profit margin to do the work.