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 ™.
/etc/torbrowser.d/50_user.conf in an editor with root rights.
(Qubes-Whonix ™: In TemplateVM)
This box uses
lxsudo for root privilege escalation and
mousepad as editor. These are examples. Other tools could archive the same goal too. If these example tools do not work for you or if you are not using Whonix, please see this link.
If you are using a graphical Whonix or Qubes-Whonix ™ with XFCE, run.
lxsudo 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.