You can. You gotta get Wireguard running on your local machine [0] and be able to see the ".internal" network, but once you do, you can ssh into any edge VM and if access its filesystem. I've SCP'd SQLite db files and dumps. It's also a pretty anti-pattern way of debugging an app if you're an outlaw :)
[0] https://fly.io/docs/reference/private-networking/