Using Handbrake for Apple TV 3: Converting DTS-HD-MA and Other Despecialized Edition Questions

I typically watch Harmy's Despecialized Edition on my TV using my Apple TV 3. I run it through Handbrake's Apple TV 3 preset and everything looks great, but I wanted to see if the community has any thoughts on all this.

1. The new DeEd includes hairy_hen's lossless soundtracks as DTS-HD-MA, which Apple TV will not pass through. The Apple TV 3 preset defaults to encoding these tracks using the AC3 (ffmpeg) option, along with a copy of each as AAC copies for devices that can't play the surround sound. (I don't usually include all the soundtracks but really wish Apple had a better way to display their titles other than "English, English, English," etc.)

Is that the "best" option? What bitrate should I be setting, or should I use its defaults?

2. The Apple TV 3 preset uses RF 20. The quality seems fine to my eyes, and the resulting file size matches iTunes store downloads. The Handbrake people seem to be pretty smart so I tend to trust their judgement on these settings but I'd love to hear some other ideas here.

3. Typically I also create a version for my iPhone using the iPhone preset, and just select one soundtrack to keep the portable file size down. A tip: if you're using Subler to add metadata, you can add a field for ContentID (I use 76759, which is IMDB's catalog number for the film, but it doesn't matter what you use). If you use the same ContentID for your HD and SD versions and import them into iTunes, it will recognize them as being the same movie and badge the file as SD+HD. Then, if you sync your iPhone and on the summary screen select "Prefer Standard Definition Videos", it'll grab the smaller file for you.

4. I also use the .srt file from Project Threepiod (en-native) as the subtitle track. My dad has some hearing impairment so it's important to me that digital files have captions.

Can anyone give a brief explanation for dummies about this DTS "core" thingy? If you can't take advantage of the full DTS-HD-MA-WTF, is the "core" as good as it gets or is it just a fallback?

What is the best way to listen to hairy_hen's mix for us barbarians that only have stereo?

If I understood him correctly, I remember him saying not to listen to the surround mix if you're downmixing it to stereo. He said there would be phasing problems--my guess being that when the surround sounds get mushed down with the front signals it doesn't match up right.

Apple TV will not play DTS files. Handbrake converts them to another format but I don't know what the quality loss is. 

Continue to trust the defaults. ;) In the past I'd do a spot check for really dark films by encoding a single chapter, and then bump the RF down a tick if too messy, but I haven't needed to do that in a while.

For high definition sources (e.g., Harmy's releases and BluRay) the AppleTV3 preset is best.

For standard definition sources (e.g., DVD) use the AppleTV 2 preset, because the ATV3 is a waste.

I'm curious about the audio phasing deal; I hadn't read about that. I had HB create the default Dolby Pro Logic track and a AC3 track from the DTS (along with the commentary and music tracks). I haven't watched 2.5 all the way through to notice anything odd. Also, while the AppleTV cannot play DTS now, you can future-proof and add it as "pass-thru".

Subler is great, especially with the new version which can search iTunes and automatically pull down the content ID. HB + Subler is such a wonderful combination. :)