User-level configuration generated probably something close to one fifth of the legitimate bug reports we received (I'm not including the people complaining about the behaviour of a check because those are probably something like 60% of all issues).
Flake8 3.x and earlier merged configuration files because Flake8 1 and 2 were built on top of pycodestyle which has the same logic. Flattening configuration in this way led to severe confusion and meant no two people working on the same codebase would have the same output.
--show-config was more-or-less implemented in our verbose logging which did it's best to help people understand the provenance of the various options.
In the end, project configuration is the most consistent way of providing people a good experience with Flake8. It means that people will all see the same results from the same version of the tool as the configuration is part of the project. As you've already found, there's nothing preventing you from specifically using whatever other configuration file you want.
I lived with the nightmare of managing and merging user configuration for nearly a decade. I'm not going back to that sheer and utter misery. It's not worth it to me. I'm not going to continue to justify it either