I'm no expert but I'll give my understanding. It's not a good idea for all the reasons you have stated. Mind you that doesn't mean it's not useful. You can use CM during the application capture process but I don't see the draw as it's just as easy to manually install apps during the capture process. There are many options to present apps in a VDI environment, App Volumes, ThinApp, App-V; but not SCCM, unless you are using persistant VM's. Not a great idea either for various reasons.