I've actually settled more on the opposite approach - my tool usage changes enough that I generally only care to configure the latest subset of tools when I get a new PC, and of course the others are there if I need them.

To that end, each tool has its own subdirectory in my dotfiles repo ( https://github.com/bbkane/dotfiles/ ), and I add READMEs to each subdirectory explaining what dependencies are necessary for this tool, what keyboard shortcuts this tool uses, etc.

This approach has been pretty resilient against my changing needs, changing operating systems, and changing tool versions; even if doesn't optimize for a single invocation of ./setup.sh