That's just the way "make install" was written. It's very
convenient to be able to completely uninstall the package
with "rm -r /usr/Local/AbiSuite; rm /usr/local/bin/AbiWord;
rm /usr/local/bin/abiword". Removing components from
/usr/X11R6/share, /usr/lib/AbiSuite, /usr/bin/X11,
/usr/local/bin, /usr/share, /usr/doc would be tough
to do by hand, and makes for trouble when the application
actually has to find its components there.
I would recommend using packages to install closely across
the system. If a package is putting things in a place
wrong for the distribution, it's a bug in the package and
can be fixed for only that package.
-- Shaw Terwilliger