Subler can't convert DTS to AC3 5.1, iFlicks is really a different purpose, haven't personally played with MP4tools or iVI.
But to reiterate, it is absolutely a stellar graphical tool for going quickly from an MKV with x264/h264 video and any audio to an iTunes/AppleTV compatible file. Every single file I've tested plays great on the AppleTV. Many of the tools out there use wrappers so that iTunes can import the video - but it's not playable on an AppleTV, this makes AppleTV compatible M4V's very fast and easy.
Does it passthrough DD 5.1? Also, if your starting file is not already h.264, but let's say mpeg2, will it still produce a working aTV file with no compression?