"base set of compiler flags" is what the Makefile and Makefile.frag is for.
If you want to have --enable-maintainer-build or something like that to enable all these warnings then you are more then welcome to do so.
This file is not portable between platforms, or even environments, since it hardcodes install without configurable path, or -j argument.
This is easily added to Makefile.frag which is the proper place for this