One more bug regarding installing Xfce into a custom prefix: when configuring xfce-utils like: ./configure --prefix=/home/user/blah the @sysconfdir@ variable is not correctly replaced in xinitrc.in.in. In the generated xinitrc file I find: test -r "${prefix}/etc/xdg/xfce4/Xft.xrdb" && XRESOURCES="$XRESOURCES ${prefix}/etc/xdg/xfce4/Xft.xrdb" where ${prefix}/etc/xdg/xfce4/Xft.xrdb should probably be /home/user/blah/etc/xdg/xfce4/Xft.xrdb. ${prefix} seems not to be replaced properly by the autotools.
I can reproduce it here. There's an easy fix for it. The problem is that the configure script replaces @sysconfdir@ with e.g. "${prefix}/etc", so when the Makefile later tries to replace @sysconfdir@ with something else it will only find ${prefix}/etc in the script and thus, not do anything. Bad.
${prefix} is a shell variable, is it set in top of the xinitrc script? In fact, it is nothing the autotools tries to replace. ${prefix} not being set results in an empty string. You should use --sysconfdir=/someone/something/etc anyway.
This is fixed in revision 29478: Use @_sysconfdir_@ and @_datadir_@ in scripts created by the Makefile in order to avoid @sysconfdir@/@datadir@ to be expanded in scripts that are created in two stages (configure + Makefile). This only affects xinitrc right now, but who knows about the future. This fixes bug #4924.