For best protection against identity correlation:
Stream Isolation
^ by following these instructions, either proxy settings are adhered one way or another (socks proxy settings or socksifier such as torsocks) or no traffic at all.
What’s better, using a socksifier or proxy settings method? Nobody is researching that to my knowledge. In Whonix, the risk is traffic going through Tor’s TransPort (transparent torification) instead thorough a dedicated Tor SocksPort. That risk is way too theoretic, obscure to anyone making it a priority to work on.
I would expect something such as orjail might be better suited for torification (non-Whonix use case) or better stream isolation enforcement (Whonix use case). orjail / torsocks as kinda “mini Whonix netwoking”.
More on orjail:
Managing programs without Tor DNS Support / orjail
Non-trivial.
Therefore asking here will probably not make significant progress on stream isolation.