Yes it can, just like the old one can. However there is a bug in the new ATV that when you go to select the different commentaries it just lists the language. So, for example, if i have a movie encoded from HandBrake with an AAC Stereo Track, AC3 Track and a Directors Commentary the new Apple TV lists them like this:
English
English
English
The old one would list them:
Stereo
Surround
Director's Commentary
The obvious bug in the new one is it is not picking up the descriptions of the tracks, but if you still select the track on the ATV2 it plays the commentary fine.