Unfortunately, there doesn't appear to be any direct way to do this with application builder. I will certainly create a product suggestion because I agree that this would be a good feature to have.
As far as a workaround, you may be required to build a wrapper around your executable that will launch a progress bar and dynamically call your main application. Of course the runtime engine and all the dependencies need to loaded first before you can actually launch a progress bar.
I would suggest taking a look at the following example, you can run this while your main app is loading: http://zone.ni.com/devzone/cda/epd/p/id/1232
Hope this helps!
Tejinder Gill
National Instruments
Applications Engineer
Visit
ni.com/gettingstarted for step-by-step help in setting up your system.