I'm sort of on the fence between spending more for a jailbroken ATV2 and its potential dedicated codecs and picking up an ATV3 on the cheap. So, what it boils down to is the assurance that most of my BD rips (non MP4's) will play nicely using PlexConnect to the ATV3 without a re-encoded of the video stream. I understand that the server would need to re-mux into an MP4, however, that's not an issue, at least not for me.
If you are talking about MKVs, they should generally play via PMS > Plexconnect with just the remux, although there have been issues reported with some individual MKVs. It also depends on the processing power of your setup. Some NAS, for example, do not have the power to play larger MKV files.
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