Video File Format: MKV container file with VP8 video and FLAC or Vorbis audio (this standard is similar, but a little more permissive than WebM, and is optimized for use on fixed media rather than downloads).
It doesn't seem like they have strong arguments to create a new standard that is almost but not quite compatible with WebM. The inclusion of FLAC is not a strong argument, rather a bad idea, cf http://people.xiph.org/~xiphmont/demo/neil-young.html
It's not just ability to use flac - there's a bunch of other restrictions on the MKV format for webm. These include chapters & menus (and ability to use separate media streams for each), support for variety of subtitle/closed caption formats, plus the ability to add attachments like fonts, textures and images for use in those streams.
Some of these features have been re-invented in the webvtt format, which is inferior to what was already available.
If they have good reason to break compatability with WebM, then they might want to use Opus (Xiph's follow-up to Vorbis) as the audio codec. It's possible that its combination of voice and wideband audio could be ideal for video soundtracks.
Opus is optimised for low-delay, relatively-low-bandwidth audio for stuff like VOIP. It doesn't make much sense for recorded media where you can quite easily hide a few hundred milliseconds of latency.
Opus is actually designed to span from low to high bandwidth (see the diagram here http://www.opus-codec.org/comparison/) and since it performed surprisingly well against aac and vorbis the developers are currently working on tuning the encoder for standard music/soundtrack type workloads at higher bitrates.
I was thinking that the mixed speech mode of Opus might be excellent for documentaries and such with lots of dialogue at Youtube or web bitrates but you're right, I forgot in this case we're talking Blu-ray size video, in which case you can just play it safe and ramp up the vorbis bitrate instead and it'll be a drop in the ocean compared with the video bitrate.
Ah I thought these features would be implemented outside of the WebM files, like on DVDs where menus and subtitles are separate from the mpeg2 files that contain the movie.
The site you linked to talks about why a higher sampling rate then what cds use is unnecessary. However, lossless audio (a different thing) is always good and is supported in DVDs, Blurays, and Cds. Lossless audio is often indistinguishable from compressed audio but is usefully when rencoding to a lossy format. (lossy to lossy will produce noticeable quality loss) Flac is a good thing and is supported by the MVK container.
It was meant as evidence that good Vorbis is indistinguishable from FLAC, but indeed the author mentions two good reasons for using FLAC. I'm not sure they apply to Lib-Ray since video will be lossy anyway, but here's what the author says on FLAC:
It's true enough that a properly encoded Ogg file (or MP3, or AAC file) will be indistinguishable from the original at a moderate bitrate.
But what of badly encoded files?
[...]
Lossless formats like FLAC avoid any possibility of damaging audio fidelity [23] with a poor quality lossy encoder, or even by a good lossy encoder used incorrectly.
A second reason to distribute lossless formats is to avoid generational loss. Each reencode or transcode loses more data; even if the first encoding is transparent, it's very possible the second will have audible artifacts. This matters to anyone who might want to remix or sample from downloads. It especially matters to us codec researchers; we need clean audio to work with.
It doesn't seem like they have strong arguments to create a new standard that is almost but not quite compatible with WebM. The inclusion of FLAC is not a strong argument, rather a bad idea, cf http://people.xiph.org/~xiphmont/demo/neil-young.html