According to @mig5
this issue should now be fixed as seen above. On an own note I managed to make https everywhere redirect from https://whonix.org to the v3 onion address. I learnt 2 things today: To do just that and that the longer onion addresses are called v3 
Adding something as an edit after I got the onebox forum achievement: Ironically I got the onebox achievement and at the same time the link did not expand into the usual stuff that one gets when one posts a clearnet link(I’ve used discourse Forums before)
Regarding HTTPS EVERYWHERE >>
With further elaboration I’ve discovered an upstream bug that affects both this browser’s https everywhere Version: 2018.9.19 add-on(inside Whonix-Workstation-14.0.0.7.4) and in the regular Tor Browser(also Version: 2018.9.19). Hitting Reset to Defaults leads to nothing changing from all advanced rules I’ve added…not even after restarting Tor Browser. I haven’t yet tried restarting the browser inside Whonix-Workstation though)