> Encrypted backups can't be deduplicated unless the encryption is flawed

This isn't an encryption problem; each device can only have one instance of Signal installed, and the latest backup (assuming it has terminated successfully) is a superset of the previous ones (aside from any messages that have dropped from retention, which you presumably don't want to be preserving, by definition).

"Deduplicate" in this context means ensuring that you only have N backups in your remote storage, rather than cumulatively storing every day.

Signal has always between one and two backups, it removes the old ones.