In most of these cases, "boilerplate" implies a choice of frameworks, libraries, build and test tools, with a minimal or recommended configuration, all tested for interoperability. The actual code advancing your application is minimal.
In the case of megaboilerplate, it appears to be a mix of configuration files plus a mini hello world built on top of the technologies. The mini hello world seems to be mostly a demo of how the chosen technologies can interoperate, not really something that "should be library code".
> Shared, standardized toolchains are harder to build but once you do they're a dramatically better long-term investment.
Possibly, but I think you underestimate the effort required to create and distribute a toolchain that would become shared and standardized. In effect, a specific team might choose a particular boilerplate, tweak it to its needs, and the tools and libraries within that boilerplate become their "standardized" toolchain.