In current autoconf there is AC_PATH_TOOL which tries both with and without the prefix, and which prints a warning if the tool is only found without the prefix and cross compiling is in effect.

My suggestion would be to replace instances of MY_AC_PATH_PROG which specify ${ac_tool_prefix} (and possibly some that don't) with calls to a new function MY_AC_PATH_TOOL, which mimics this behaviour (but which is implemented using AC_PATH_PROGS), except that I think binaries without prefix should be ignored rather than warned about when cross-compiling. There is nothing wrong with having "freetype-config" installed when cross-compiling, so it does not warrant a warning, but using it for the cross-compilation will give incorrect results, so we shouldn't.

Something like this:

define(MY_AC_PATH_TOOL,[ if test "x$enable_binary" = "xno"; then AC_PATH_PROG($1,nobinary_dummy,$3,$BINDIR) elif test "x$cross_compiling" = "xyes" -o "x$ac_tool_prefix" = "x"; then AC_PATH_PROG($1,${ac_tool_prefix}$2,$3,$4) else AC_PATH_PROGS($1,${ac_tool_prefix}$2 $2,$3,$4) fi ])