This is strange.
It doesn't happen in my MSYS2 installation.
I'm wondering why your gcc is considering /usr/include/stdlib.h and so get confused about the realpath definition.

I think the proper location of the header is /msys64/mingw32/i686-w64-mingw32/include/stdlib.h and there is also no definition of realpth and so no problem.

$ gcc --version
gcc.exe (Rev1, Built by MSYS2 project) 9.2.0
...
depbase=`echo tm_source_file.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/sh ../../libtool --silent  --tag=CC   --mode=compile ccache gcc -DHAVE_CONFIG_H -I. -I../..  -I. -I../../ctags/main -DGEANY_PRIVATE -DG_LOG_DOMAIN=\"Tagmanager\"  -mms-bitfields -pthread -mms-bitfields -IC:/msys64/mingw32/include/gtk-2.0 -IC:/msys64/mingw32/lib/gtk-2.0/include -IC:/msys64/mingw32/include/pango-1.0 -IC:/msys64/mingw32/include/fribidi -IC:/msys64/mingw32/include -IC:/msys64/mingw32/include/cairo -IC:/msys64/mingw32/include/atk-1.0 -IC:/msys64/mingw32/include/cairo -IC:/msys64/mingw32/include/pixman-1 -IC:/msys64/mingw32/include -IC:/msys64/mingw32/include/freetype2 -IC:/msys64/mingw32/include -IC:/msys64/mingw32/include/harfbuzz -IC:/msys64/mingw32/include/libpng16 -IC:/msys64/mingw32/include/gdk-pixbuf-2.0 -IC:/msys64/mingw32/include/libpng16 -IC:/msys64/mingw32/include -IC:/msys64/mingw32/lib/libffi-3.2.1/include -IC:/msys64/mingw32/include -IC:/msys64/mingw32/include/glib-2.0 -IC:/msys64/mingw32/lib/glib-2.0/include -IC:/msys64/mingw32/include -DGLIB_VERSION_MIN_REQUIRED=GLIB_VERSION_2_32 -DG_DISABLE_DEPRECATED -DGTK_DISABLE_DEPRECATED -DGEANY_EXPORT_SYMBOL="__declspec(dllexport)" -DGEANY_API_SYMBOL=GEANY_EXPORT_SYMBOL -g -DGEANY_DEBUG -g -O2 -MT tm_source_file.lo -MD -MP -MF $depbase.Tpo -c -o tm_source_file.lo tm_source_file.c &&\
mv -f $depbase.Tpo $depbase.Plo

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