A few quick comments on the XML format level upon skimming this (mostly nit-picking):

- you don't seem to identify the namespace URI in the normative text, it's hidden in the RNG schema
- you don't use the namespace in your examples.
- the example in 3.4 doesn't follow the specification for the description element:  You either need a CDATA construct, or you need to entity-escape the pointy brackets.
- in the specification for the description element, don't talk of "CDATA" as an element.  It isn't, but rather a particular way to mark up textual data:
 http://www.w3.org/TR/xml/#sec-cdata-sect
 So: The content model for <description> is text; if content includes markup, then CDATA is a convenient method to write that out.
- MIME-type -> media type

- To the unique identifier point in your issues list -- agree that it might be useful to give the table a unique identifier.  I probably wouldn't choose an ID attribute, but would include a "this version" and "latest version" URI in the <meta> section.

- I may be missing something, but what's the extension model for the @when attribute on <var>?  Are certain names there reserved for IANA, and others up for grabs?  Want to use URIs for these names, so everybody can coin their own without stepping on others' toes?  Something else?

Hope these are useful,