I tried this myself a while ago, and the startup image showed up according to the storyboard, yes! I don't think there was anything special I had to do, except adding the file to the IPA and referencing it in the application XML via the "launchScreen" tag.
If you want, I can try again to see if it jogs my memory as for any non-intuitive steps.
I have to say, though, that I couldn't get AIR to create a seamless startup experience when using the storyboard. There was always a short flicker when the storyboard image was replaced with the first AIR-rendered frame. For this reason, I had to resort to the old PNG files. :-/
That doesn't have to be relevant for every app, though. In my case, though, the flickering was just too annoying.