"And what if a pre-assembled PC is cheaper than your custom built PC by $300-$400 provided certain minor things are inferior to your custom PC? "
Then I would assume that those "minor things" really add up to features worth $300-$400.
One can easily see processor prices, ram prices, to compare. If you pay cheaper assembled for the same components not assembled, they would be losing money!
You are paying for pre-assembled name and perceived quality, and most importantly turn key convenience, on top of thier profit margins of course. There is no way it would be cheaper. I worked assembling PCs and CPUs are not *that* much cheaper in bulk. Maybe if you are dealing in tens of thousands of CPUs, but why would the company give up all that profit? You are paying for a service, no way its going to be cheaper.
Another way to think of it is like oil changes. Sure you can go down to the local garage and get an oil change for $30 bucks. However you get their cheapest margins filter, cheapest oil, and they get to look and see what problems are under your car and recommend solutions (@ their prices). Your car will probably still work when they are done and run fine. So many people choose this option. Doesn't mean its cheaper for the same components, because its usually not an apples to apples comparison @ their price points.
If you want to get the good oil, good filter, they will charge you more for that. Might as well do it yourself (buy oil, quality oil filters, or computer hardware, when its on sale). If you have the skills and care about quality of components, then its the only way to do things. Plus you get to look over the rest of the machine for other problems or targets of opportunity. As opposed to a technican doing that, who may or may not be correct in their diagnosis. May or may not be honest with you.