The article really seems to be more about "so you want to design a custom PCB for a given embedded Linux capable application processor". While it is full of useful information and candid findings, there is usually negative business value in this approach as Jay admits lower down the article: I don’t think most people design PCBs around these raw parts anyway — the off-the-shelf SOMs are so ridiculously cheap (even on…
The only thing that SOMs provide is a processor + DRAM + PMIC. If you practice and become proficient at designing around application processors, it should take you no longer than 3-4 hours to get this component of the system (the processor, DRAM, and PMIC) laid out when working with these entry-level parts.
SOMs aren't some magical remedy to all the problems. It's still up to you to design the actual system, which takes hundreds of hours. The difference between using a SOM or a raw-chip design is negligible at this point.
I have no problem prototyping on EVKs --- in fact, I link to EVKs for each platform in my review. But a lot of these evaluation boards are pretty crummy to prototype with; some don't have all the pins of the CPU brought out, others use proprietary connectors that are a hassle to adapt to your hardware. You shouldn't be afraid to spend an 8-hour day designing a little breakout board for a part if you're interested in using it in a product that's going to span 6-months' worth of development time.
Of course there are caveats. I'm entirely focused on entry-level parts; if you need a Cortex-A72 with a 128-bit-wide dual-rank DRAM bus, sure, go buy a SOM. Also, it should go without saying that it completely depends on you and your company's core competencies. This article is aimed at embedded designers who are usually working on hardware and software for microcontroller-based platforms. If you work at a pure software shop with no in-house EE talent then this article is likely not relevant to you.