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My experience is that in most cases people clone modules just to get extra main menu items. It would be better if the main menu was a bit more flexible, but cloning modules to do this is a very long way around the problem.
As for two XOOPS sites off one install, do a search for the multisite hack by bd_cmsc. I don't think he ever got it perfected, but I beleive it is functional for the most part.