Even if it does, transfer to a disposable sys-usb-android and from there to wherever would be the least dangerous way. If it’s possible, dedicated USB controller to this sys-usb would be preferable.
You can use Syncthing. Sync a directory on the phone to a directory in an AppVM. The syncthing inside the AppVM connects out to the Syncthing on the phone. The connection is encrypted and the clients are open source (packages available in f-droid and debian). The connection can be done over a local LAN (no dependence on a 3rd party service).
Going to second airelemental’s suggestion. Just use Syncthing. Set up a shared folder on your phone, and then set up the same share folder on your VM of choice. As long as your sys-net and your phone are on the same network, everything will just sync.
I sync my phone’s storage using Syncthing. I don’t even have to think about it — every photo I take and every note I change is automatically synced whenever the phone wakes.
EDIT: who wants to write a tutorial? I would gladly publish the tutorial on my site.