On the Stream Isolation page, there is a list of applications that are pre-configured to use socks proxy settings using application configuration files. If you want to disable this...
You must go to the applications settings and remove what Whonix has applied by default.
TODO: document, expland
For some applications this is impossible.
Those can only talk to Tor Hidden Services directly. You cannot configure them to use the system default. You can only deactivate sdwdate and/or not use Ricochet IM.