Yes, manpages are installed into both MANDIR and LIBDIR.  The output of 'man mafft' depends on $MANPATH.  On linux, the installation directory can be /usr/local/ (from source) and /usr/local/ (from my rpm package).  If a user installed mafft from the source and then installed a new version by the rpm package, there are two different versions installed.  In this case, the output of 'man mafft' can be inconsistent with the version the user uses, unless the user is carefully adjusting the consistency between $MANPATH and $PATH.

So I added an option, 'mafft --man' which displays the manpage that was installed together with PROGS.  At least by '/usr/bin/mafft --man' and '/usr/local/bin/mafft --man', the manpage of the correct version should be displayed.  (But I'm not frequently updating manpages.  I have to do it.)