Have you considered adding a CF instead of a mechanical drive? There's all sorts of ways, SCSI-to-IDE bridge, SCSI card reader, one of those homebrew CF adapters that mounts underneath the processor with the five zillion page long thread on Amibay, etc.
In my limited experience adding hard drives to Amigas, I never had to mess with a mountlist entry, I always just configured them through HDToolbox and away I go. Not sure how you'd do this under 1.3, I assume your controller has some special software for prepping hard drives that works under 1.3? You may want to read up on the documentation and limitations (if any) for your particular controller before making a decision. Maximum partition size, etc.