The directories mentioned in the documentation are not variable and thus when
they are changed at build time (as debian does) the documentation and the
behaviour differs.
There is debian bug (725804) for this.
I could not find a clean way to change this as afaik the build variables are not
available in the .texi files. The only variables I found come from version.texi
and it is unclear to me where that file comes from.
But I think a solution could be adding something like
echo "@set SYSCONFDIR $(sysconfdir)" >> directories.texi
...
in the makefile and include / use those in the texi files.