I agree with a lot of stuff in here (have been sort of working on my own approach to the problem which is similar to some of the stuff you mention).
However I’m not sure boilerplate is quite so pernicious, depending on what you mean by boilerplate. I suppose the problem is that a lot of beginners are grabbing Webpack config boilerplate that is equivalent to those “Ultimate VIM configurations” that do absolutely everything according to the very specific wishes of a very advanced developer.
When I first started using Webpack my config file was about 5 to 10 lines. entry, output, a loader or two….and that was fine. If people are willing to make boilerplate projects for beginners and beginners are disciplined enough to choose them over the ULTIMATE version then i think a lot of these problems go away. And in the long run we can come up with more sophisticated solutions to these problems.