When you add media to a person, fact, citation, etc you have the option to link to the media or copy the media into the Family Tree Maker Media Directory. If you link, instead of copy then the only thing generated is a link to your media files in your Dropbox Folder. Then, when you backup the file, don't include the media.
Have you looked into this? I think it will do what you want but am not entirely sure.
Have you tried doing this with a small test tree just to see what will happen?