Right now, the two versions are identical (although their version numbers differ). I hope to keep it that way, but it may change once I submit a sandboxed version.

In general, the sandbox doesn't cause us any problems, because we already write our temporary data to the proper sandboxed location, and dragging a file into an app is one of the approved sandbox interactions. However, enabling the sandbox DOES break QuickLook icon fetching for some types of objects (most notably volumes, which show up as folders). This seems to be a bug in NSWorkspace that I hope will be addressed in the future.