Now that Whonix bind-directories has been upstreamed to Qubes as bind-dirs.sh (T414), Whonix needs to actually start using it.
Inquiry when bind-dirs.sh will be available in Qubes R3.1 or R4.0, done:
https://github.com/marmarek/qubes-core-agent-linux/pull/58#issuecomment-213114874
The difficulty here is to smoothly transition away from Whonix bind-directories as soon as Qubes bind-dirs.sh gets available. Perhaps Whonix bind-directories should check if Qubes bind-dirs.sh is available and terminate when it is? Then the config file for Qubes bind-dirs.sh could be deployed right now and no user of R3 / 3.1 / 3.2 / 4.0 should run into any issues, right?