In both Workgroup Manager and Profile Manager, you can drop in arbitrary plist files to be delivered to clients. If an application gets its preferences from MCX will it automatically work with Profiles?
The end result of applying a profile are traditional plists in the /Library/Managed Preferences, so it is conceivable that third party managed preferences will perform just the same with this new/additional delivery method. I have used localMCX in Lion for Office2011 prefs without issue, and tested other Apple manually applying profiles with the /usr/bin/profiles command. I find delivering Apple's managed preferences with profiles lack the granularity I was used to in the past, but there are some new features you wouldn't be able to as easily interact with otherwise.