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

My (limited) understanding is that sys-net mostly just serves as an interface for the network card to channel data to sys-firewall (which then sends it to sys-whonix). I’m sorry, my level of understanding is not sufficient to answer with any certainty.

This guide and related discussion might provide helpful information.

Perhaps you could copy your questions over to the whonix forums ? The devs over there have been very helpful with my whonix on qubes related questions.