Thanks for the detailed bug report.
1, 2, 3:
The bridge returns an error due to too many requests, which was introduced in an update by Hue. Same as Windows app is not working anymore, where I added some retry logic which improved the connection. I will try to optimise this further. Do you by any chance use any other software simultaneously which communicates with the bridge, e.g. any other apps, scripts, or automation software? I noticed the bridge returns this error when too many apps are communicating at the same time, which could be the case here. Not sure at the moment how that could be fixed, but will look into it.
4:
Correct, the group containing all lights was always shown in Hue Essentials. So, many users use this and created scenes/effects in this group. Unfortunately, this group has disappeared in the new API, so scenes/effects could be removed in the future. This is why the app shows this message, and new scenes/effects cannot be created. It uses the old API for this group for now, which could stop working in the future. I still have to think about migration, but this group will probably be removed in the future. Replacement is just creating a zone with all lights. For now, you could hide the group (under the three dots at the top of your screenshot).