I do understand how you want to preserve your file structure but there is a way to keep the media folders separate for restored RootsMagic database's with media. You could restore one database with media and then rename the media folder. Then when the next one is restored with media rename that media folder that is created. You would either use List>Media Gallery>Tools>Fix broken media links or Search>Search & Replace>Multimedia filenames to fix the broken links.
Thanks for this, Renee! Being able to redirect all the media in one batch is wonderful!