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.
TODO: document and expand.
Remove proxy settings for Tor Browser Downloader by Whonix.
Open /etc/torbrowser.d/50_user.conf in an editor with root rights.
If you are using a graphical Whonix or Qubes-Whonix with KDE, run.
kdesudo kwrite /etc/torbrowser.d/50_user.conf
If you are using a graphical Whonix or Qubes-Whonix with XFCE, run.
kdesudo mousepad /etc/torbrowser.d/50_user.conf
If you are using a terminal-only Whonix, run.
sudo nano /etc/torbrowser.d/50_user.conf
Paste.  
For some applications, this is impossible:
These applications can only talk to Tor Onion Services directly and cannot be configured to use the system default. You can only deactivate sdwdate and/or not use Ricochet IM.