That was it! My bad, I installed the duplicati service, therefore the database has root owner.
Using sudo allowed me to lauch the desired compare. So, copying the 2.0.4.5 update folder from /usr/share/Duplicati/updates to ~/.config/Duplicati/updates works.
So, the remaining issues are:
- updating via GUI puts updates in /usr/share/Duplicati, while the cli looks into ~/.config/Duplicati/ . This, on Ubuntu 16.04, having installed the deb of beta 2.0.3.3 from the website.
- Doing a Restore from the GUI throws a series of yellow warnings without explanation (however, this could be related to https://forum.duplicati.com/t/what-does-it-mean-to-report-a-duplicate-path/1997/16)