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Not only does a module reduce implementation complexity dramatically, standardization skips every engineer potentially making their own dumb component placement mistakes.And we've never found a way around that for the decades we've been putting Atmel, STM, TI, Ambiq, Nordic, etc chips in our designs... There's an intern 2 yards away from me who will be wrestling with getting the right components in place around an STM, for his very first pcb design. This is not a hard problem for anyone who has been doing this for any period of time.
And anyway, those dozen or so components are the oscillator/crystal circuit, the reset holdup, and the 3.3v supply. And then like a bazillion decoupling caps. Certainly, antenna tuning can be hard, but if you can use chip antennas, its not that hard.
All of those are so bog standard that when I looked at e.g. the adafruit RP2040 Feather's schematic, I was sort of surprised at how much is just lifted wholesale from all of their other feathers. Like, the only difference between the RP2040 feather and the nRF52840 feather is the micro itself, the timing circuit (all 5 components of it for the RP2040), and the antenna circuit for the Nordic board.
As to the convenience of modules, I submit that they are very handy for sale to the hobbyist market, but if you want to actually sell your products, you still have to go through the process of RF certification (although at a lower cost. Only you can decide if the higher upfront cost of using a module vs. spinning your own is offset by the lower certification cost), so the benefit is a lot more mixed. Even so, you're only saving the antenna tuning step, which is usually done as a BOM variation, not a major trace adjustment.
As to the dozens of STM and PIC chips, TI has the same situation. Customers want to pay for only what they need and those manufacturers have the manufacturing capacity to support that desire. Its not daunting if the difference matters. This is very much akin to complaining that Home Depot sells too many different kinds of lumber.
As for capacitive touch ICs, sure Adafruit only carries one. But mouser carries 199 that are not end of life. To keep that functionality going, adafruit need only pick up one of them. The cheapest one is even in a TSOT package, so the DFM will be pretty easy. Hell, if I'm not too tired from my job designing and programming these things, I might go home and spin one up tonight. Ought to only take me an hour or so. And the I2C driver another couple hours.