For every $500 or so in parts, boutique builders tack on about $100 over retail. They'll also mark up common parts.
Their advantage is they buy in bulk when it comes to components and OS. So they are actually making a little more on top of that.
On the very low end, this can make it more economical to buy from a retail store and add a discrete GPU. But once you are above $700 or so it makes far more sense to build it yourself.