I tried to replicate this issue with my debugger attached on MacOS. It works exactly as I described above, picking up the ~/.config/Duplicati/Duplicati-server.sqlite file, until I place a file in ~/Library/Application Support/Duplicati/Duplicati-server.sqlite.
It may have been fixed in the latest source code as I consolidated some code that was looking for the right configuration folder in two different ways.
I will try to fix the Ubuntu %HOME% issue you found and then I will make a new canary build (2.0.9.105).
Before you install 2.0.9.105 on your other system, can you please check if you have these files prior to installing the new version:
~/.config/Duplicati/Duplicati-server.sqlite~/Library/Application Support/Duplicati/Duplicati-server.sqlite
You should have the first one and not have the second one if you have not tried a version after 2.0.8.1.