To fix access to onion apt-repositories the following solution works. (apt-transport-tor fortunately not required.)
/etc/apt/apt.conf.d/30user
Acquire::BlockDotOnion "false";
I am wondering in which package to ship such as config file. anon-ws-disable-stacked-tor is not perfect, since this needs to be applied on gateway and workstation.
(Probably uwt got into the way. For your curiosity perhaps try apt-get.anondist-orig. 
)
Can you shed light on gnome shell vs performance? //cc @HulaHoop