LUM_User is kept seperate intentionally and besides that there is only one variable for the prefix which the forum uses. I was under the impression that the setup script asked you what prefix you wanted to use but maybe it doesnt. In which case I suppose that aught to be added in future versions...
I've actually had a hard time with this recently. I'd love to hear any insight people have to integrating Vanilla with other applications, and what kind of adverse affects the vanilla setup had in this regard.
I had a major problem with integrating Vanilla and Drupal, as you can see in my Doc, I had to hack Vanilla's core to get the LUM_ prefix removed from a table that isn't the User table, it was very annoying... and will make upgrading that little bit more difficult on my forum.
I was thinking, why not hardcode the prefix into the appg/database.php file's $DatabaseTables variable like you do with LUM_User, this way you can override the table names with whatever you like! Surely that is more advantageous than hardcoding it, it isn't confusing either.