Great question, I spent a lot of time thinking about that. Eventually, I realized that it
wasn't convoluted to work from my Dropbox folder. At least the problem wasn't keeping project files there. After all, most projects are just lots of source code, and it doesn't matter where it sits.
The big problem with keeping projects in there is that each project might have computer-specific configurations. I try to keep those to a minimum, by e.g. using relative directories whenever possible. For the few things that I can't keep completely relative, I rely on environment variables that I set on each computer I work on.
Other than that, I haven't run into any problems working right out of my Dropbox directory. At one point I considered running all my software from Dropbox (using portable versions), but that really did cause a lot of headache (most programs have session-specific configuration which would cause problems on different computers).
Have you run into any other problems with keeping projects inside Dropbox?