I'm doing some work in OSX and some in Windows.
So I've downloaded the OSX & Windows bundles and got both Projucer binaries in the same folder.
Why not just distribute a single bundle? It would make it easier to maintain, and would emphasise the fact that the bundles are identical save for the ProJucer build.
Another handy feature would be having the ProJucer update itself and keep its JUCE modules up-to-date.
This would mean having ProJucer store a 'path to modules' string as an application property. Individual projects would inherit this by default but could choose to override. But automatic updating would only apply to this path.
ProJucer could even display the most recent commits on its homepage.