In a large complex project build scripts tend to take on many tasks, and some of them will not necessarily fit into the pattern of taking in a stream of file globs, modifying them and piping them on into the next task. For example your script might manage a Git repo, deploy an app to Heroku, rsync some files somewhere, run some tests in a headless browser etc. So a build system that's optimised around streams, and one that you have to script by hand, might be very well suited for small streamlined projects but once things get varied and complex it might better be better to define your tasks via configuration instead of code, i.e. Grunt.

Also most automake is a combination of automake and shell (sometimes it's hard to tell which is which).

That is one way to do things, I think the wrong way. If you need something more sophisticated your build system should have a way to write code that is testable and then used declaratively in your build. The answer should not be scripting in your build file.