I have a relatively simple use case, but I get around this by having all my folders in Dropbox and setting up symlinks outside Dropbox that point to the folders

I have a relatively simple use case, but I get around this by having all my folders in Dropbox and setting up symlinks outside Dropbox that point to the folders in Dropbox. If you want to sync default MacOS folders that you can't delete in Finder (Pictures, Movies etc.) you can delete them using sudo in terminal and recreate them as symlinks. I've even done that with Desktop (I just keep plain text files there) and it's been working fine for a few years now.