Hello Claus T Neilsen,
It will work, but it will always fall back into compatibility mode when backing up, and unzipping. This is because it doesn't have access to command line zip. There are possible workarounds for this. Below is a link to the BackupBuddy Codex, specifically the server recommendations portion. I'd review this information, and consult with your host.
Please let us know if you have any other questions!