Our users like this feature on non-persistent multi session, but the issue we're facing is the apps (office, explorer) launch before wem has finished processing. Anyone have a suggestion on how to get the system to relaunch apps after wem has applied its config?

Not sure if this will also delay WEM from starting but you can try different settings with the following reg keys:

[HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\Explorer\Serialize] 
"StartupDelayInMSec"=dword:00000000 
"WaitForIdleState"=dword:00000000

Most people use these keys to reduce the time it takes to launch startup apps but I don't see why you couldn't do the opposite.

I will try this out. I forgot about this key

Or use the external task to restart the apps?