I'm not sure about the playback capabilities in OSX... however all of the latest HD formats are now supported by the MKV container and are (under Windows at least) fully accessable via FFShow and a few others.
I'm not 100% sure of the conditions/settings for MakeMKV (haven't researched yet) but I would guess that the audio is either preserved in it's pure format or is converted to FLAC and then passed to your processor/receiver as an LPCM stream - there *might* even be an option to determine which method was used. But I'm not totally sure on that.
I've never bothered trying to use my Mac as a media frontend - I consider WMC (in Win7 at least) to be about the only piece of Microsoft software that even comes close to being worth the hassle of the OS. That plus I love MediaBrowser - even if it is pretty buggy... it's freakin' beautiful.