Would help to quote specific things.
https://trac.torproject.org/projects/tor/wiki/doc/TorPlusVPN talks very little about Whonix. Quotes I can see:
You -> your own (local) VPN server -> Tor
“your own (local) VPN server” means a different implementation. Similar to Whonix. Instead of using the dual VM architecture of Whonix, one might be able to use a VPN to locally force all traffic to go through Tor. This is using VPN technology / OpenVPN perhaps. This doesn’t reference using any remote, commercial VPN servers one can purchase. Aka
TorVPN. Details here:
If you want this, it may unnecessary to use VPN, a simple Tor-Gateway may be easier, for example Whonix.
Let me translate. That means
“If you want this, it may unnecessary to use local (!) VPN (TorVPN. A simple Tor-Gateway may be easier. For example Whonix provides a Tor-Gateway.”
The other quote:
- If you still want to combine Tor with a proxy, all combinations are possible using Whonix (anonymous general purpose operating system). Whonix’s optional configurations document this.
It’s true. Anyone who insists on combining Tor with VPNs can do so using Whonix.
https://www.whonix.org/wiki/Tunnels/Introduction documents this.
However, while Whonix ensures that Tor will be used and has documentation how to use a VPN “for real” (speak: no leaks) using a fail closed mechanism… None of this indicated that Tor acts any special on Whonix. See also:
Does Whonix ™ Modify Tor?
The the purpose of this question: “No”.
Therefore I don’t think there is anything Whonix specific in this question. Therefore this question could also be researched as per https://www.whonix.org/wiki/Free_Support_Principle.
If you want to configure Tor in unique and discouraged ways, Whonix does not limit that.
Other Tor related questions unspecific to Whonix can be redirected at the Tor support.
As far I know and experienced for long running connections such as to a IRC chat server, Tor does - usually - not change the circuit in order to not interpreter the connection. It tries to do that. A connection user -> Tor -> VPN would be similar to a IRC chat server connection. Usually. Meaning if a Tor exit would be (briefly) offline or unreachable, the long running connection would be interrupted. Tor would open a new circuit - probably using another Tor exit relay. And the application (IRC chat client or VPN client) would reconnect and thereby ending up using the new Tor exit relay.
So unless you hardcode only 1 Tor exit, you risk that VPN servers see connections coming from different Tor exit relays.
Quoting the conclusive from https://www.whonix.org/wiki/Tunnels/Introduction
For the vast majority of Whonix ™ users, using Tor in isolation – without a VPN or proxy – is the correct choice.