In Tor Messenger case... No worry about Tor over Tor. [Because it's also tor-launcher based.] [Because Tor Messenger has been thought ahead at Whonix development earlier.) (Similar to https://www.whonix.org/wiki/Tor_Browser#Whonix_Proxy_Settings.)
Instructions similar to https://www.whonix.org/wiki/Manually_Updating_Tor_Browser. Download. Verify. Extract. Start. Done.
Would anyone like to formalize these instructions in the wiki?
Also https://www.whonix.org/wiki/Manually_Updating_Tor_Browser#Introduction mostly doesn't really fit there.
Install by default.
For now there are no plans to install it by default. Hopefully it will be installable from official Debian repositories soon. Otherwise installing software outside of apt-get by default is problematic. Difficult to keep updated while preserving user settings. Once installable official Debian repositories, installation by default should be a piece of cake.