CARMACOMA  Actually it's kinda works that way, I think, at least it worked for me and later I talked to their tech support. So when you get iPhone "pushed" you need to press "synchronize" button in the bottom left corner, and (as I was told) if you have repos in your InstallerApp program, it will check what apps you have on your iPhone and will download them to the computer as well  
(Version 1.0.1)

CARMACOMA  Really nice app, exactly what I was looking for — now I can restore iPhone and then put back all non official apps with a few clicks. really impressive work for 1.0 though I expect more features in the versions that will follow.  
(Version 1.0)