Before using borg I would recommend you to take a look at restic. In my opinion it is better in everything than borg.
As for how to backup the database, my advice is to export the database to a SQL file and backup that file. That will always be easier than having to deal with agents that connect to the database.
As for the number of repositories, if you use restic, a single repository is enough. Besides, as restic does deduplication, if you have the same files between your machines, they will only occupy the space of one. ;-)