I was reading about Tor over Tor, it says When a transparent proxy is used (like in Whonix), it is possible to start a Tor session from the client as well as from the transparent proxy, creating a “Tor over Tor” scenario. This happens when installing Tor inside Whonix-Workstation or when using Tor Browser without configuring it to use a SocksPort instead of the TransPort.
Disabling transparent proxying is a good way indeed to prevent any Tor over Tor scenario. This is now mentioned in documentation.
What really needs to be done is disabling the internal Tor of these applications. In that case, there is no need to disable transparent proxying, which is just safety net to avoid Tor over Tor.
Configuration of an application to use a Tor SocksPort:
B) doing that for an application that ships its own internal Tor to use a `SocksPot but without disabling that application’s internal Tor might actually still lead to Tor over Tor.
Unfortunately, making applications that come with their own Tor integration (shipping their own internal Tor and/or using Tor control protocol) compatible with transparent proxying and/or Tor-split (VM) solutions (such as Whonix) is in the realm of developers; often requires research, writing documentation and sometimes even upstream source code improvements.