Interesting as I have found the opposite. We have 18 core programs deployed with each OS deployment. I have seen the deployment time drop from 1.5 hours down to 45 minutes or less when all the programs are contained in a single wim. It seems that the main difference in time can be placed on deploying Office 2007 w/SP2 which takes forever to install independently.
"1. Deploy Windows 7 including applications from the SCCM server. Are there any requirements or limitations when using this method?"
I have a wim that is 13.5 gigs that contains a mapping program that if installed manually takes over 6 hours to install per system. When it is contained in the wim along with the other 18 programs the user is logging into the domain within an hour going to work. Before it would take over a week to prepare a classroom of 30 computers using multiple people but now a single person walks around the room hits F 12 enters the PXE password and selects the image and within an hour they are ready to go.