The "original" 9-bit fixed-point encoding isn't widely used; most formats use a 32- or 64-bit float, or the number encoded as a string. One of the Matroska developers posted on the HydrogenAudio forums[1] saying they use a 32-bit float, but the spec he quotes later[2] is different than what's on the actual Matroska site.
Do you know if the cover.jpg standard is documented anywhere? Searching for "matroska cover.jpg" just yields a bunch of bittorrent sites.
[1] http://www.hydrogenaudio.org/forums/index.php?showtopic=7294...
[2] http://www.hydrogenaudio.org/forums/index.php?showtopic=7294...
I think cover.jpg came from doom9 [1]
I guess robux4 was talking about the old system, which I honestly didn't know existed before you brought it up. If the new system doesn't use the 16 bit format then yeah, it isn't well specified.
[1] http://forum.doom9.org/showthread.php?p=388815#post388815
Cover art wasn't specifically defined in mkv I think, but it became standard to do an attachment named cover.jpg for it.
The spec on ReplayGain seems pretty clear to me: it's the 16-bit binary format defined at http://replaygain.hydrogenaudio.org/rg_data_format.html which is two links away from the mkv spec.