This would completely defeat the point of Dropbox, then; If your Word document is in your Word folder, how does it get to another computer? Do you give the app developer, Microsoft, exclusive right to 'sync' your files elsewhere?

Sandboxing is a good idea. An old idea, actually; chroot was added to unix in 1979. But shared filesystems evolved and are the norm, and even if many apps could be sandboxed, Dropbox exists outside the sandbox for a reason.