Hi,
You can have multiple skins for your site and you can have different skins on different pages. In Site Settings just enable Page Skins. To change the master page just change the skin.
In mojoportal design is abstracted at the skin level. I implemented the skinning system with one master page per skin as that was sufficient to achieve the needed skinning and keep complexity at a minimum. If you want to use more than one master page within a skin I don't have a good answer for you.
Hope it helps,
Joe