Tor with VPN on router

Qubes-Whonix
1

Which way is my traffic going when using VPN installed on physical router:

  1. User → VPN → Tor → Internet
    or
  2. User → Tor → VPN → Internet

What are the main drawbacks of such configuration?

2

This. The VPN connects first. Everything else in on top of that. It is similar to using a VPN on the host operating system.

If User → Tor → [...] was possible in that configuration then the VPN setup would be broken.