> I'm probably wrong but I think what's happening is this:
> Look up the process list and you'll see the invocation:
> su -l user -c /usr/bin/xinit.......

Right

> That's su starting a shell as a login shell: as you have zsh as default
> shell, .zprofile is read to set env variables, including path.
> 
> And I think you should have seen the output from qvm-run ps aux
> included something like "sh -c ps aux".

Right

> That call to sh is coming from qrexec-fork-server, I think.
> 
> I hope that makes it a little clearer.

Not too much, but I guess I lack some background in qubes internals :)

> It would be interesting to see what happened if you were to relink sh
> to zsh in the template. I'm looking at a number of issues arising using
> some non default user shells(tcsh, fish)

Doing so:

$ qvm-run -a -p qube "echo $0"
# => sh

$ qvm-run -a -p qube "ps aux"
# Inclues
# => /bin/bash /usr/bin/qubes-session
# => su -l user -c /usr/bin/xinit
# => ps aux (without `sh -c` before)

$ qvm-run -a -p qube 'echo $SHELL'
# => /bin/zsh

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