On the Stream Isolation page, there is a list of applications that are pre-configured to use socks proxy settings via application configuration files. To disable this, the Whonix system default must be removed from the application's settings.
TO DO: document and expand.
For some applications, this is impossible:
These applications can only talk to Tor Hidden Services directly and cannot be configured to use the system default. You can only deactivate sdwdate and/or not use Ricochet IM.