I have 100+ Apple TVs in my district that need to be configured for deployment within the next month or so and over the last 2 days I've been having issues with the new configurator and also the Apple TV 6.0.1 update. In configurator 1.4.0 I would connect the Apple TVs via USB and they would be detected under the Prepare tab. In the newest update they are no longer appearing under there, but under the Apple TV Assistant instead. Beforehand I had been installing the updates on the apple tvs and then going back and updating the names of them (As they all have to have different names) which was easy, but now the only way to name them is through the Apple TV Assistant, but you have to erase IOS in order to do it. See the below procedure as to what is happening:
1. Apple TV Assistant detects Apple TVs and installs updates on each of them under the naming convention that I created.
2. Apple TV Assistant installs IOS 6.0.1 on each Apple TV and then asks me to reboot each of them.
3. After Apple TVs are rebooted, it checks activation, supervision state, and then fails at "Updating Device Properties" error given "The Operation Timed Out." "Code -402653172" "com.apple.mdk.amderror"
Apple's supposed fix is this: "If you install Apple TV 6.0.1 while installing profiles, you may see a delay of several minutes while the profiles are being installed, or the profiles may not be installed. If Apple Configurator reports "Unable to update device properties" you will need to reinstall the profiles separately. Complete the setup assistant on the Apple TV manually, then use Apple Configurator to install profiles, choosing "Don't Install" in step 4 above."
However unless I am missing something, there is no way to name an apple TV via profile, so they would still have to manually be named.