On the Stream Isolation page, there is a list of applications that are pre-configured to use socks proxy settings via application configuration files. If you want to disable this, you must go to the application's settings and remove the Whonix system default.
TO DO: document and expand.
For some applications, this is impossible:
These 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.