Installing applications is a rare event, updating them is frequent, and needs to disrupt the user as little as possible. Android used to not allow alternative app stores to update apps without user interaction, but now supports this through UPDATE_PACKAGES_WITHOUT_USER_ACTION, which doesn't seem to be supported by F-droid. So it's manual clicking for each update.
F-droid also somehow gets the regular update flow wrong and often (always?) shows an error when you try to install the update from the notification. That has remained unfixed for years. So you have to manually open it, initiate the update, then click through the dialogs.
Additionally, the official repos update so slowly that they're useless for fast-moving stuff like NewPipe.
Together with Android bugs like https://issuetracker.google.com/issues/204233247 (resetting all "open with" URIs on update), this makes using packages installed through F-Droid a nightmare.