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.
Obviously lots of applications it would be impossible to use a 264 bga but I've been there with projects with 3 CAN buses and Ethernet plus flash memory and thought maybe we should be using a cortex A7.
I'm sure you know but file storage on microcontrollers can drive you insane ha ha and the same with graphics+TCP IP
Zooming out to a broader management context, non-trivial systems usually comprise multiple processors. In these circumstances production volumes are generally lower and subsystem iteration more likely, therefore it makes more sense for managers to worry about overall architecture (eg. bus selection, microntroller vs application processor, application processor architecture) and consider factors such as speed of prototyping, availability of talent, longevity/market-stability of vendor's platform, feature-set and nature of software toolchain(s), etc. rather than worry about optimizing specific processor part selection.
The management priority generally only flips closer to the article's fine-grained approach in the event that you are designing a consumer electronics widget or otherwise very high production run product with a low change expectation, where individual processor selection and BOM optimization become greater concerns.
Conclusion: For most people, for most products, most of the time, you don't want to start by worrying about specific processor part selection. Further, prototyping should be done on third party dev boards/SOMs and when production volumes justify it, final PCB design can be handed to an outside EE. This is not always a viable strategy (eg. due to form factor or other application constraints), but it's fast, cheap and hard to go too far wrong.