I’ll have to rip and transfer another DVD to be sure, however the one DVD that I’ve tested has a bonus feature that’s 16:9, and that appears stretched as well. MP4 files played through the standard AppleTV video player don’t have this issue, regardless of aspect.
The AppleTV video output is set to 1080i.
Update: I’ve transferred another DVD, from the same publisher / content creator, but it has both 4:3 and 16:9 playback options. 4:3 is stretched as before. 16:9 also appears stretched, except that there are black bars on both top and bottom. (I’m fairly certain that you can at least see the side portions of the image in the 16:9.) A different 4:3 DVD from a different publisher has the same stretching problems.
I also have several 4:3 aspect mp4 files converted with Handbrake and transferred via iTunes that play correctly through the standard AppleTV video player.