Well, I for one don't have a problem with the article. Even if you take all the caveats into the equation, you can still build a superior system with Win 7 and discrete graphics. If you had to build a new system (instead of using the SBM $500) configured to compare to off the shelf models, it really wouldn't change anything. The conclusion is still valid. If you have to include Win 7 in with the price, you're left with $430. It can still be done and will still be superior. Also, you'll have more parts to upgrade with over time -- for instance, the SBM $500 could easily accept a Phenom X6, or a Sandy Bridge setup, or whatever comes along in the future. The ram, hdd, psu, case, and gpu will all work for quite some time. That won't work with the store bought systems. If you change the mobo and cpu (you won't really be able to upgrade the processor anyway) in the Dell, you'll probably have to get a new copy of Windows too, not to mention the nonstandard cases.
I'd kinda like to see what's available from the smaller systems makers of the world, and take that into account. I for one wouldn't want it any other way than to build my own. And if building budget systems themselves aren't that exciting, I enjoy the challenge of working in the budgetary constraints. So, keep up the good work -- I'd like to see more of this in the future.