How about bind-mounting ~/.xbindkeysrc.scm outside the chroot into /var/host/xbindkeysrc.scm or something and sourcing it?  Not adding it to this patch, but it would provide a simple and consistent way to extend xbindkeys for all chroots.

The other thing to note is that xbindkeys may need to be replaced if it's disappearing from Debian and causing issues with VNC and whatnot.