Yes, this is certainly doable, with for now the limitation that for all items within a menu the location and size parameters of the objects must be the same. For example, the system characters in the main menu can be different per system as you want, but they will be at the same x/y coordinates. I would suggest placing all theme graphics in the layout directory, so if your layout is called "dougan", place the graphics in layouts/dougan/collections/<system name>/system_artwork, and use the modes "layout" and "systemlayout".
Main menu reloadable images per system: Use mode "layout", and put the images in your layout directory.
Collection static images: Make a copy of the main menu object, and use mode "systemlayout", and it will use the same images as the main menu reloadable images.
Collection reloadable images per rom: Skip the mode attribute, and leave these images in your normal collections directory.
If you run into any trouble, just drop me the XML code, and I'll have a look.