In automake 1.9 (debian package) manual, the "Public macros" node on
AM_PATH_LISPDIR says
Searches for the program `emacs', and, if found, sets the output
variable `lispdir' to the full path to Emacs' site-lisp
directory.
This reads like lispdir will be the emacs path, like /usr,
irrespective of what your own package's configured --prefix is.
But if I'm not mistaken the macro in fact simply chooses between
$libdir/emacs/site-lisp
$libdir/xemacs/site-lisp
$datadir/emacs/site-lisp
$datadir/xemacs/site-lisp
according to what flavour and setup $EMACS has. Ie. it's always under
your $prefix, just in a varying location there. Perhaps the
documentation could be reworded to make this clear.
Incidentally, is $libdir only for old versions or emacs, and/or old
style filesystem layouts? If that's so maybe that could be noted, or
describe $datadir/x?emacs/site-lisp first and then the $libdir second,
or something like that, so current conventions are shown first, if you
know what I mean.
