The only disadvantage I find is that there is no cross system deduplication.

You could achieve this by having all machines write to a single Borg repository, where everything would get deduplicated. But downsides include: 1. You lose everything if something goes wrong with that one repo, and 2. You’d have to schedule backups across all systems so as not to run at the same time, because the single repo can only have a single writer at once.