There were early efforts to port Whonix to Qubes R2 by a specific user.
Prior to that Qubes used a TorVM - a small qube that proxied network
traffic to Tor.
As I remember WhonixQubes left the project very shortly before
integration was announced. I found that odd. (You can read this in the
mail archives around April 2015)
There were perceived to be issues with updates using the TorVM - the
hope was that Whonix would solve these issues (Ha). There were also
perceived benefits in linking with a project that provided a focus on
anonymity. Reading the mailing list archives is the best way to get
background on this.
I dont use Whonix - among other reasons, I find it unwieldy and a resource
hog. I use a TorVM - packaged at https://qubes.3isec.org. It’s a base
package that you install in a minimal Debian template (or clone), that
provides a Tor gateway: no traffic is passed in the clear. Unlike Whonix
it supports the Qubes firewall. It runs with about 400M.