As an electronic design engineer, it just feels to me like these kind of things aren't really huge problems day-to-day...
In terms of decoupling designs etc., the reason nobody has come up with a better solution is firstly that it doesn't actually take up enough time in the scheme of things to bother, and secondly that you often have to deviate. For variable regulators for example, the output capacitor (and inductor if it's not included in the device) are chosen based on output voltage, the switching frequency you choose, and sometimes other variables. You often want to deviate from the recommended circuit in the application notes for various reasons.
I'd think of a circuit board production as more like putting together a magazine than working on a software codebase, where you'd have a bunch of people working on overlapping parts of the code.
I mean even for a lot of boards we do (even quite complex ones) we'll just have one design engineer and one layout engineer, but for things where multiple people work on the schematic we just have people work on their own sheets and then somebody brings them together into the final design - kind of like where you might have an overall designer/editor that pulls a magazine together but individual people having put together individual articles. But it's pretty common that it would still be mostly laid out by a single engineer unless you're doing something extremely complex...