Add some minor reorganization to the Makefile preamble

The gist here is a reemphasizing of the explicitly "user mutable" bits by putting them first (and hopefully improving readability a little bit in the process).

This builds on #9152, but I figured a new PR after his merged made more sense than making @duglin go back and forth with all these minor changes since I wanted to do a little bit more than his PR was even touching. :smile: