EDIT: WARNING - As usual for me, a much longer than expected response....END WARNING....
As someone who does this type of thing every day, I too will side with mouser on the price. I find Dell, HP, etc. quite a bit more expensive - usually due to warranty and support offerings that smaller integrators don't provide (though they do tend to offer more personalized experiences that allow for similar effects). Comparing my Newegg purchases and build with a local computer shop came up with prices about the same with more "risk" associated with it. The "risk" I speak of is in the area of incompatibilities. However, my experiences also point to 99% of those inocompatibilities stemming from a few avoidable sources. 1) Not doing the research. If the equipment is not brand new to the market or VERY niche, then there is almost always a good base of compatibility testing available. Check forums and such to find if there is anyone who has had issues with it in the past. If you don't find ANYTHING about it, it is likely okay. That leads to 2) Don't buy anything so new to the market that no one has tested it yet. This seems like a no brainer, but if you do buy it, you are in for headaches. Which leads to 3) If you buy it anyway, look for firmware updates. Firmware updates frequently fix incompatibilities with the hardware. As the system matures, the firmware makes the hardware work nicely with other hardware.
I learned this lesson the hard way on my first system. I bought a new motherboard that looked great on paper (specs). I shortlisted several video cards and found one was by the same maker as the motherboard. Among other reasons, I chose that video card because of the likely compatibility from the same manufacturer. Can anyone say microsoft compatibility testing? Needless to say, the motherboard was bleeding edge. I started it up several times before I went back to the old PC to look up the website. It was sparse, but I found WinXP pre-install drivers (who knew I needed those

) and more importantly, the firmware update - 4 versions newer. With those pieces of software installed, WinXP worked like a champ. Within 2 months, 3 newer versions came out to allow all my SATA drive connectors to work. Apparently there was a bug in the second SATA chipset that was onboard. Good thing I didn't try using that

. Anyway, I learned from this experience and my work experiences what I stated above. If you like the bleeding edge, be prepared for that. If not, just stick with popular hardware that meets your specifications, and do your research.
Oh, and on the article - they are right about the simplicity of it all. It is the research to ensure compatibility that is a pain. Once you know the system will work together, the actual construction is a breeze. Also mouser, there is a second reason to build your own. So you can match the specs to your needs. Of course a local computer store that will actually listen to you could do so too, but they usually don't listen because the brands and models your research provided for you to specify are not their standard offerings...