A 1280x720 encode with a custom anamorphic setting keeping the aspect ratio the same will play fine on the ATV2. However, you will not get as much bang for your buck as you would get playing the same file on the original ATV or on a Mac. Those devices can output 1080p and can take advantage of the extra resolution.
The ATV2 is limited to 720p output. So even if you have 720 horizontal lines on a wide screen movie the ATV2 is going to have to scale it back down to 555p or whatever to maintain the aspect ratio. So, it can play the 720 line encode just fine, it just cannot take advantage of the extra resolution yet.
Assuming ATV2 is never capable of ever outputting 1080p and is always limited to 720p, and you never plan on viewing the same encode on any other higher resolution device, the there might be an advantage in using the preset in that the lower resolution can result in smaller files sizes and save HD space.
However, that is a big assumption. The original ATV could not output 1080p initially, but that feature was added latter through a software upgrade. The ATV2 is even more capable hardware, and same thing could happen with 1080p being added by a software upgrade.
I use the 1280x720p custom anamorphic setting because I still have an original ATV that I use regularly. The files play fine on both versions and the higher resolution is definitely visible with the original ATV.