Programmable Microcontrollers vs. SoC Devices
The short answer is: Overhead.
Yes, an SoC running an OS has more resources and can do more. The tradeoff is that the hardware and software then become significantly more complicated than a dedicated microcontroller running custom firmware because they have more overhead.
Hardware overhead means a more complicated board design which may require:

More board space (more expensive and may not fit product form factor)
More support components (more expensive)
More PCB layers (more expensive)
Higher quality PCB manufacturing processes (more expensive)
More time spent debugging due to more failure points (more expensive and can cause schedule slips, and may still result in buggy hardware shipped to customers)

Software overhead means that there is more code and a deeper software stack (e.g., a Raspberry Pi has boot firmware, a kernel, hardware drivers, system daemons, and your user applications), potentially spread across multiple hardware components (e.g., the WiFi/Bluetooth and USB/Ethernet driver chips on RPi run their own firmware, whether or not you intend to use those features). More software always means a higher risk of bugs, which can cause operational failures, poor and/or unbounded performance, and compromised security. For small-scale and hobby deployment, these tradeoffs can be acceptable. For mass-produced products made by even a moderately reputable company, it’s a no-go; there are simply too many variables that are not in the manufacturer’s control.
Even if you are using an off-the-shelf SoC board, like a Raspberry Pi, which spares you many of the hardware development and production costs above, you are risking failure in the field by using a (relatively) bloated software stack.
An additional factor is how much control the manufacturer wants to have over their product and supply chain: If you’re basing your entire hardware and software design around a massive monolithic block from a third-party vendor, you are tying your fate to that vendor. Supply disruptions, cost increases, vendor hw/sw bugs, and deprecation are all risk factors.