This might seem slightly off-topic at first, but bare with me, it gets increasingly on-topic.
What kind of e-mail are you trying to download over Tor though? Like in general, Tor hides who you are, but not necessarily what is send/received at exit/enter nodes. If any encryption, like SSL/https is poorly handled, i.e. by the server/website you visit, then it's not enough security through Tor exit/enter nodes. So for example, if your e-mail has at any point, whatsoever, in any way, been leaked with information linking it to you, or giving any clues that a detective can use to identify you, then it's game-over for that e-mail address, and you need to make a new address.
Though it depends on your needs of course, for example if you don't care about governments, large corporations, or resourceful hacker groups, but only want to hide from the regular typical everyday hacker and businesses, mass surveillance, etc. then the e-mail is not compromised and can still be used on Tor.
Aight, so the point, what exactly do you want to hide your e-mail from? In my experience, there are different approaches to different scenarios, which includes e-mails too.
More specially towards the question at hand, I think it's tricky to do something like that in Thunderbird, but I'm not a programmer, so I wouldn't know for sure. However, if you think about how it works in Qubes/Whonix/Tor, then the Tor browser appears to be tunneling Tor-Browser within Tor(Sys-whonix), basically doubling the onion layers compared to a regular Tor browser. I'm not entirely sure if this is the case, it's just something I figured must be the case.
In other words, when you do this exit node change in your Tor browser, this does change your exit from your Browser, but not the exit node from your sys-whonix Tor network. Basically, the middle link between the two onion Tor layers, remains the same until it changes on its own automatically like usual.
In other words, the Tor Browser can do this, because it itself is tied directly tor the Tor network. But for applications, like Thunderbird, it has no means to communicate with the Tor network, and it seems unlikely something the whonix developers, or the Tor developers, would want to implement given the extra overhead or potential issues introduced through further complexity (but I wouldn't know, I'm guessing towards that).
Also this is probably a better question asked on either the Whonix or Tor forums, probably most fitting for the whonix forums. The people over there know waaaaaay more, unless if lucky and one of them happens to drop by here.
Not sure what you mean by "AppVM level" but "New Identity" marks ALL circuits dirty regardless of where it's invoked. So using "New Identity" in anon-whonix-6 is the same as using it in sys-whonix for purposes of generating new circuits for Thunderbird. TorButton (in Tor Browser) performs a few additional tasks as described in link below compared to arm, but as it relates to circuits, they both send SIGNAL NEWNYM.
https://stem.torproject.org/faq.html#how-do-i-request-a-new-identity-from-tor
https://www.torproject.org/projects/torbrowser/design/#new-identity
ah, good I made a disclaimer :')
Though, it does seem rather unsafe to run multiple of qubes over the same exit nodes in the Tor network.
The most dangerous security issue out there, imho at least, is the assumption you are safe, when you are not. If what you're saying is true, and I'm confident it is given your background, then this might cause some dangerous user habits on Qubes in particular, beyond that what is a concern by using just Whonix/Tor? Similar issue probably exits between Whonix and Tor, but to a lesser extent as Qubes does not have any warnings about this, which is particular a concern when it's easier to mess up in Qubes, and run the same applications over the same exit nodes, at the same time.
I did hear the warning of not running Tor over Tor before, though it was so long back that only the Tor browser was around back then. I had assumed it'd been fixed by now on Whonix and in particular Qubes. Especially considering the dangerous trap Whonix and in particular Qubes creates when running more on the same exit node.
ohh, I see, so that's what is meant by "circuits". It does give the word an interesting meaning, albeit it might common to understand it correctly in an institutional context within the Tor community. But the essence of the word does make sense too in this context after explained.
Thanks for the clarification, as you probably know it would, it changes how I perceived the Tor network quite fundamentally.
I apologize for my wrong assumption that I thought the Tor network as a single channel at any given time. It never occurred to me that it could have parallel channels in a different circuit kind of way.