I think Thunderbird should go through Tor just like APT. While Kicksecure and Whonix both serve different design goals/purposes, I think other applications in Kicksecure should take advantage of using Tor by default like APT already is.
These “Apps” should be Kicksecure specific since if the same configuration were on the same Apps on Whonix WS it would cause issues like Tor over Tor or not working etc.