This is “normal” behavior with the current version of Duplicati on DSM, and is definitely not good behavior. The root filesystem is small, PLUS it tends to get wiped out during major DSM upgrades. There is an open issue about it, but it has not been resolved yet.
Back when I ran Duplicati directly on DSM, my solution was to use a symlink. I now run Duplicati in a docker container and don’t have to deal with that issue any more.