Hi there,
I thought I would just share a conversation I had with the Akeeba Backup guys.
Their professional version will backup the moodledatadirectory (above public_html) using their directory inclusions feature. Therefore you can install Moodle with both the moodle database in a separate mysql database and the moodle data directory (moodledata) above public_html.
This should give you the technical flexibility and provide you with a single operations process for backup and restore.
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