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I use the Droid-ify client and rarely get issues: https://f-droid.org/en/packages/com.looker.droidify/

I get the F-Droid toasts once every few weeks or so. To me, it's worth it. Finding a tolerable weather app on the Play Store is impossible nowadays. Finding one on F-Droid is easy.

Same problem here, but only for a few apps (e.g. signal)

I have never seen this error, and auto updates do work for me.

They are a blessing when auto updates were finally possible with the official F-Droid app.

You might consider one of the alternative front ends. Won't fix the repos being unavailable, but will fix notifications about it.