Good news, I think this one's finally sorted: the cleanVm: incorrect backup size in metadata warning was fixed in XO 6.4.0 (released end of April) via PR #9637, which makes incremental remote backups record the actual VHD size instead of the slightly-off metadata value.
If you're on 6.4.0 or later, it should be gone, so worth confirming your version and upgrading if you're behind. @manilx, you were waiting on this one.
