I've had better success with auto-update using Driod-ify. At the very least the client downloads the updates automatically so it's just a matter of tapping install.
I'm not entirely sure tbh. Like I said, mixed results depending on the app, but my working throey is that the session installer can automatically install apps that have the same signature and don't require any changes in permissions. I've seen some apps do in-place upgrades with no user touch but some don't.
On Neo store, f-droid front end, in the settings there is an option to auto update all apps. Also has a one click button to update all apps if you don't want to auto update.