Well, they are the "core" utilities after all. This becomes less of an issue the further out in the ecosystem you get.

> at the exact versions and in the exact locations on the filesystem that the build tooling is willing to look.

This isn't strictly true.. you just need _compatible_ versions to be available, and most build tools and even the compiler itself will check several commonly used locations for code.

There are a few corner cases, but by and large, this isn't as big a problem as it might be for other languages that make writing incompatible interfaces orders of magnitude easier than with C.

> Specifically, hasten the day where my entire application dependency tree doesn’t bottom out in some Autotools, CMake, shell script, project.

Each those solve the same problem at different levels. Perhaps this is because there is no _one true_ way to replace them, and the advantage is that each project uses the tool most suited to their case.

Perhaps the built-in tools with these "modern" languages are a good general tool for the majority of developers, perhaps they aren't. If they aren't, then now you have the same problem all over again in a new ecosystem.