I would love to know this also. The only way I've found is to temporarily remove the device(s) from the configuration profile, make the settings change that's desired, and then add it/them back to the scope and reapply the profile. Pretty annoying.
As long as I'm wishing for features, Apple, I'd love to have the ability to control sleep and screensaver settings on AppleTVs with a configuration profile.
That is the primary reason we are going into Single App mode so there definitely isn't any sleep or screensaver kicking in. Manually removing and re-adding isn't very helpful when dealing with thousands of them all over the year.
In our case, I'm replacing all of our AppleTVs this summer with ATV4s. So I'll have to manually walk each one of them through some settings changes before being deployed. Then, I can push the profile that locks them into Single App mode. This will prevent my users from modifying settings, so I won't have to mess around with manually setting up restrictions like I did with all our ATV3s. AirPlay still works, even with Single App Mode enabled. Sleep can be set to never, and the Aerial screensaver still kicks in. Other than losing the ability to use any other App that might be requested (YouTube? Vimeo? Whatever), this seems like a pretty solid solution for us to:
1) Lock down the AppleTVs
2) force them to launch into the Plex App, so my users can still get to our digital media library
I can even remotely reboot them.
I only wish we had more management controls via configuration profiles. And, I wish we had the ability to push an App via VPP (rumored to be coming very soon).