I decided to come back to this and check whether this premise would hold up for a lower-end system. I used AVADirect, since they had the highest savings over the enthusiast DIY build compared in this article. I then looked to their "Budget Gaming Desktops" section, and picked the "AMD B350 Budget Gaming Desktop" configuration to base my comparison off of, which cost $729 (without an OS), and came to $761 shipped. The components for that base build are as follows...
CPU: Ryzen 1400
GPU: GTX 1050 (EVGA)
RAM: 8GB (2x4GB) DDR4 2133 (Kingston HyperX)
Mobo: Prime B350-PLUS (Asus)
HDD: 1TB 7200 RPM (Seagate BarraCuda)
PSU: 400 Watt (EVGA)
Case: Corsair Carbide 100R w/ Window
Like the article, I limited my pricing to Newegg and to be as fair as possible, I picked the exact same brand and model of components when available, which I was able to do for everything except the PSU and RAM, in which cases I picked the lowest-priced name-brand components with similar specs. So how did it compare?
I was able to find the same components on Newegg for just $597 shipped, which is $164 less than the custom shop build. Their version of the system cost over 27% more than if you assembled the hardware on your own. That's not necessarily a bad price for someone who doesn't want to mess with putting the system together themselves, but what could $164 more get you?
CPU: Ryzen 1600 (+$52)
Not only does the 1600 get you 2 more cores and double the cache, but also a more substantial cooler to help you get more out of overclocking.
GPU: ZOTAC GTX 1050 Ti (+$47)
The price of the 1050 Ti might be inflated more than that of the regular 1050, but it does offer faster performance and double the VRAM, and unlike any higher-end cards, some are still available that aren't nearly double their launch price.
RAM: Team T-Force Vulcan 8GB (2 x 4GB) DDR4 3000 (+$0)
Ryzen's performance can benefit from higher speed memory, and DDR4 2133 isn't even up to the standard 2666 speed for the platform. This DDR4 3000 kit is on sale for the exact same price as the lowest-priced 2133 kit at Newegg, so nothing is added to the cost. Otherwise, it might have added around $10 more.
Mobo: ASRock AB350 Pro4 (+$0)
More positive user reviews and more connectivity options, including a USB Type C port and a second M2 slot, potentially useful for future upgrades, at the same price after rebate.
HDD: 2TB 7200 RPM Seagate BarraCuda (+$15)
For just 33% more than the 1TB model, you get double the storage space at the same speed, making it a cost-effective upgrade.
PSU: Seasonic S12II 520 watt (+$7 -$15 rebate = -$8)
A higher capacity PSU from a quality brand for a lower price after rebate.
+SSD: ADATA Ultimate SU650 120GB (+$45)
It's a small SSD, but should improve OS performance and also have enough room for a small number of regularly played games.
Case: Phanteks Eclipse P400 Temperered Glass (+$10)
I put the remainder of the difference into the case. The existing case was a decent enough budget option, but it wasn't much to look at. The P400 is arguably a lot nicer looking with its tempered glass side panel, open layout, PSU shield and RGB lighting, and it also comes in a variety of color options. It does lack external drive bays which could be a downgrade for those who need them, but overall it seems to be a better design than the Carbide.
So, for the same price as AVADirect's "Budget Gaming Desktop", we were able to move up to a CPU with 50% more cores and a better cooler, a faster GPU with more VRAM, faster memory, a slightly better motherboard, double the HDD space, a better and higher capacity PSU, a much fancier looking case, plus we added an SSD. And we technically had about $3 to spare that we can put toward the trouble of having to fill in a few rebates. Now how much would a system like this cost at that site? I made some changes to their base build, selecting the lowest-priced similar components, but was still limited to slower DDR4 2400 RAM since they didn't offer anything faster for this build. Still, the updated build ended up costing $943, and $976 with shipping added, which works out to $215 more, a similar 28% increase over building the system yourself.
I should note that unlike the article, I did not include tax, since Newegg only collects tax in 5 states, so that won't apply to most people in the US. If you're going to include tax on the Newegg order, it would only be fair to include it for the custom shops as well, since just like Newegg, they charge tax in certain states where they have a physical presence. So, how would the prices compare for those builds from the article with the difference in tax taken out of the equation to keep everything on a level playing field? Based on the article's pricing, the Maingear one would now cost over $200 more than DIY, the Digital Storm would cost over $300 more, CyberPowerPC would be priced about even and AVADirect would show a savings of only around $150. And again, that's dependant on the volatile pricing of these graphics cards, where pricing and availability can change significantly from one day to the next.
The premise of the article isn't necessarily wrong for a high-end system built by these companies, and even in cases where it costs more, it might be worth it for someone who wants an all-new build, but doesn't want to spend the time ordering parts, assembling the system and potentially troubleshooting things. In the low to mid-range though, those on a budget can still likely make their money go a lot further with a self-built system.