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, run.
kdesudo kwrite /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.
TB_NO_TOR_CON_CHECK=1 needs to be set because there is no filtered Tor ControlPort access when Whonix tunnel firewall is enabled, which would break tb-updater's Tor connectivity check.
By tb-updater default, if unset, variable
CURL_PROXY will be dynamically set to a Tor SocksPort on Whonix-Gateway. For example to
By using a curl parameter we are using anyhow, i.e.
CURL_PROXY="--fail" we can in effect disable the environment variable even if it's technically still set. This will result in downloading by using the system's default networking.