Thanks for the options Jon.
I've used a number of those apps in the past, but my primary need when I sync video (which I do a lot) is to use it where streaming ins't available or reliable, so I need to be able to copy them locally. I've been a video collector sine the days of VHS and Laserdisc. We have a very large collection of discs which have all been encoded to mp4/m4v, and I have no intention or 'retrofitting' all those files to work correctly with the new Apple TV. I also don't want to do something that 'breaks' the video so it doesn't work across all of our devices using the native apps, which makes me reliant on a 3rd party app which may or may not be around/work in a few months. I've gone down that road before and the result was me switching apps every few months so that everything would continue to work correctly, which my family did not appreciate.
Manually selecting the track is annoying, but not my biggest issue. The fact that I can't get both Dolby Pro Logic and 5.1 to work on a single set of Apple TV TV / Amplifier settings is a significantly bigger issue. If the Apple TV is set to Dolby Surround all our 2 Channel Video plays as stereo, and won't decode into Dolby Pro logic correctly, so we actually have to change both Apple TV and Amplifier settings each time we switch from videos that have only 2 Channel AAC audio versus videos encoded with 5.1 (which is about half our library). That totally *****, especially since we didn't used to have to do a thing and it just worked correctly. It's broken, and Apple should fix it, I shouldn't have to 'fix' my library every time they release a new product.
The fact is, for anyone who encodes their own content, the Apple TV 4 is an incredible disappointment. I'm mad at myself for not returning ours (we bought 3) when I had a chance, instead of trying to fix all the issues. Broken audio, Siri not searching your own library, descriptions set via iTunes don't work, etc.. The list goes on. Not that I should really expect anything different by this time. Each generation of Apple TV has focused more on online content and broken or buried the features that who build their own content libraries really need or want ... but that's what you get from a company who doesn't believe in focus groups and whose employees think bandwidth is ubiquitous and that everything you'd ever want is stream-able ...