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. :)