I can now confirm that v12.0.24 fixed the de-duplication issues seen with separate web and email servers. I won't share the command to run though, as it clearly says to only run it at the instruction of Enhance Support, but it does fix it.
Anyone having issues with excessive disk space use after updating to v12, with email and app/db roles separated, just drop an email to support and with the given command it's fixed in a few seconds.
In this case, it is on a separate block device with BTRFS, as per the default setup on v11 and before, confirming that no conversion to ext4 is required to continue to use the efficient backup system as it was before.
12.0.24 - New ecp CLI tool to synchronise http enabled status across all servers.
This was the magic fix for people waiting to upgrade due to possible overflowing disks on their backup servers.