Qubes Debian templates have non-free/contrib (apt) by default

Indeed, strictly speaking, it’s not true. However, Qubes is free and open-source to a similar degree as Fedora or Debian are. Both are not endorsed by the FSF, while trying to avoid the blobs as much as practically possible.

From the Fedora web page:

Fedora creates an innovative, free, and open source platform

From Debian web page:

Debian is a complete Free Operating System!

Should they also change their wording?

The Qubes FAQ already explains that Qubes is not 100% free. I personally think that it should also include a list of non-free software, so anyone would be able to remove it if they wish.

See also: Is Qubes fully free? and Does Qubes meet the GNU FSDG?