I’m not an android dev nor am I affiliated with the f droid project so this might be wrong: As far as I know f droid started using an Android built in mechanism for updating. It has to request permissions to install and update apps at all and then it has to ask once for each individual app.

So you allow it to update apps and install X. Then once X gets an update you will be asked whether f droid is allowed to install ist. When the next update for X comes f droid will be silently allowed to install it.

As far as I understand it’s just how this kind of permission works on android.

Maybe it has to do with the new feature https://f-droid.org/en/2024/02/01/twif.html

Fdroid only gained the ability to auto update apps a while ago, so that's why you got that prompt.

Also, if the permissions an app requests change, fdroid can't always auto-update it.

You have to grant permission to update each app one single time and then after that it will no longer ask you to manually update that app anymore as it will just be able to do it. For apps that are very commonly updated you will see this once and then not again. Some apps are rarely updated and when everything else has been updated automatically you'll still get this one app that has not been and needs permission.

Look at the notes about the update. It will say what permissions have been changed. It is provably just the base android permissions have changed by adding a feature that has altered what your previous permissions were set at