I had this question asked to me the other day so I thought I'd write a quick article on it. You may have noticed that Compressor does not create H.264 files with timecode tracks when using the Apple Devices presets.
The reason for this is that MP4 and M4V files do not support timecode. However, the MP4 specification is based on the QuickTime file format so it's easy to create a QuickTime movie (.mov) instead of an MP4 and the file will still be recognized by iOS devices and the Apple TV.
To do this, simply add an Apple Devices preset to a file and then change the file extension to mov in the Encoder tab of the Settings window. Compressor will then create an iOS and Apple TV-compatible H.264 with a timecode track.