Can ISP still detect Linux (or Qubes) if sys-whonix handles everything except the physical NIC?

This setup is seen by your ISP as a TOR traffic.
If you do it correctly, then that’s it, no other traffic should be seen by any observer outside of your Qubes OS device.

However doing it ‘correctly’ (means: there 101% no leaks) is really hard - if not impossible in practice.
So I would be not depending on the Qubes OS defaults for sure. See this topic for more:

Moreover, If you want to ‘blend in’ using TOR is very likely not the way to go.

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