The Free Software Foundation, the organization behind the GNU project, has been unifying the build procedure for its tools for some time. Thanks to its tools ‘autoconf’ and ‘automake’, most packages now respond well to these simple steps, with no other intervention necessary:
./configure options make make install prefix=/usr/local/stow/package
Hopefully, these tools can evolve to be aware of Stow-managed packages, such that providing an option to ‘configure’ can allow ‘make’ and ‘make install’ steps to work correctly without needing to “fool” the build process.