The distribution builder assumes distribution of the final, release build of an application, but you can get around this by including the debug output file specifically (like any other file) instead of the symbolic, "Project Name Output" file item. The only disadvantage to this is that the file will be tracked by absolute path, so if you move your project directory around, or change your output path in the Target Settings, you'll have to fix up your distribution settings. A (somewhat hacky) way around the absolute path issue is to add the file to your project (Edit>>Add Files to Project>>All Files...); this will cause it to be tracked relative to the project.
You make a valid point about sometimes needing to debug the application on a different machine, so I encourage you to file a Product Suggestion if you feel debug distributions should be directly supported.
Hope this helps.
Mert A.
National Instruments
