My first computer was a NEC prebuilt, my 2nd a "custom order from ABS," and my 3rd a Compaq prebuilt. The NEC was my first learning computer. By the time the 2nd came around, I had learned enough to order what I needed... but not put it together myself.
A Christmas price discount put the Compaq prebuilt (with a 3 year complete warranty) at the same price point as another custom order.
2 years ago, I decided to start building them myself due to the ability to get better quality and faster components, including warranties with each component. Since then, I've built an "enthusiast" gaming pc for myself, an "enthusiast" gaming pc for a friend, and 2 "mainstream" gaming pcs for other friends.
I am currently finishing an "enthusiast" gaming pc for another friend (an i7 920 build), and I am about to order the components for 2 other systems. (An office/net use pc for my mother and a home theatre pc for myself.)
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For all of these, the OPs method of comparing what you get from a mainstream maker (Dell, HP, etc), to a "custom order" maker (ABS), to building from components has been done. Since that Christmas special so long ago, several hundred dollars has been saved on every gaming pc build. (And, for the builds for friends, I tell them upfront that I pocket any/all mail-in rebates from the components as "payment" for my time.)
For the "about to be ordered" components, the price difference is much lower. However, the difference with these systems is their quality, overall loudness, and "future-proofing."
With a computer from a mainstream maker, you cannot... in the future... typically upgrade:
1. The case (Motherboard mounting holes are drilled incorrectly.)
2. The Motherboard (See above)
3. Easily upgrade video cards (Due to the lower powered Power Supply)
....
In short, a mainstream computer is built to never be touched except for the potenial adding of a 2 sticks of ram, an extra hard drive or two, and maybe an extra DVD drive.
From a custom maker, you fix the above issue.
Thus, if the OP wants the comfort of a complete unified warranty from a company he can trust, I say go for it. (I did with ABS in the past, and I don't regret the decision.)
However, if you are ready to "take the dive" and build... including possibly repairing and diagnosing issues mostly on your own with limited/possibly unreliable Internet forum help... then take the plunge as well.
There are benefits to the 2nd and 3rd approaches. I, however, will never buy another "mainstream" maker desktop again. (Maybe one day we'll be able to build our own laptops too.)