Like with anything else, you have to "shop" a little bit to get exactly what you want. MicroPro was just one suggestion. Unlike WalMart, you probably could talk the sales guys at MicroPro into giving you a 5% (or more) discount on your order. The reality is that all wholesalers and retailers, especially those with computer gear, are having difficulty moving inventory right now. Why else do you think that Intel and AMD are delaying the release of the newer/faster CPU's? Watch the "Orders vs. Inventory" numbers on CNBC and it can help you determine when the best time to buy hardware is regarding price.
You get what you pay for. was never more true than it is with computer gear. Check out that off-the-shelf box and see if you can add a faster CPU, or even a second one. See if the MB can handle a high end graphics card by disabling the on board video (some you can't disable). See if you can determine who manufactured the components in the first place. On a support level a year or two later, this can be a LARGE issue. A few MB's are also TOTALLY INCOMPATABLE with some high end graphics and sound cards, not to mention applications. (YES, this DOES happen!)
In the late 80's I bought a 486 DX50. It was the fastest thing going at the time. By doing a custom order, I spent an additional 100 bucks to get an EISA motherboard instead of ISA. The EISA MB was a small server board and had true 32 bit throughput instead of 8 bit. It also had one of the first flashable BIOS chips on it. It benchmarks like a P-120. I still have that box in my office and use it occasionally for a plot server or for word processing if my other machines are tied up with other users or tasks. I spent a little extra on the front end and it has really paid off as time has gone by.
With a custom order, you will also get full hardware documentation and drivers for every component. This too can save you a bundle of headaches a year or few down the road. Don't assume that you will always be able to find those things on the Internet. I have an 8 Meg video card and a 10/100 network card sitting beside me on my desk that we have not even been able to determine the manufacturers of, despite all of the sophisticated search methods. That is going to cost my client money. She will now have to replace two components that we could reuse if we knew who made them.
Best of luck with your purchase.
Sleeping Dog