I use droidify and there was a permission it asked me for to be able to install apps in the background. It still sometimes gives me the pop-up but usually just installs the updates after clicking update (I don't like automatic updates).
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I think with automatic updates enabled, they seem to install automatically without confirmation. I usually wake up every few days to a notification that a few apps updated overnight.
Every now and then I'll need to confirm an update, but most happen unattended. I don't know why there's that discrepancy
I might misremember but I think it only happens if its the first update triggered by auto update. Once that's done, the future update for said app wouldnt ask for permission no more.
It might be the F-droid client you are using doesn't support auto-updates?
I've personally switched to using Obtainium