Enable "auto fetch updates" for new users, encourage old users to enable it.
Now that the workflow for notifying about updates is much improved with the new UI, we should actively encourage people to enable the feature.
The default value for "Automatically fetch updates" should be switched to true for new installs of F-Droid.
It would be relatively trivial to add a banner at the bottom of the Updates screen when the user doesn't have this feature enabled. Something to the effect of "All updates must be downloaded manually. Would you like to enable automatic downloading of updates?".
It may also be of use to display a subtle message at the bottom if they do have this preference enabled. This may say something like "Updates will be downloaded automatically".