When I do build though my shop, there are tons of things to consider.
parts cost, and rma on any warrantied parts.
quote cost. Taking the time to custom build the pc per customer's wishes.
labor cost, how much is my time worth?
bench time... Taking away from diagnosing on the bench. 1 custom build takes up the space of 3 towers running diagnostics easily.
Then, you are practically married to that person. Every virus, pop up, and software incompatibility is YOUR fault. This adds labor to the build almost every time because kissing ass makes more money than not.
Some of the builds I find on clist are actually only on a 5 - 10% markup from parts cost. That is pretty low considering. Dude's an asshat.