Trellis doesn’t adjust the Vagrant default mentioned above, so unless you adjust share folders in the Vagrantfile or move your Vagrantfile, I think you’ll always find Trellis files on the VM at /vagrant.
See if this thread addresses the issue: Running deploy within the guest VM on windows : Issue with building assets - #2 by fullyint
If any new issues come up and you’re stuck, go ahead and start a new thread.