It's an oversight. The changes should be accompanied by version* directives. I see you already committed a change for compileall.rst - thanks for that! Please feel free to add anything you find missing or submit a bug report and assign it to me.
The PEP 3149 commits did not touch Doc, apart from sys.rst which got its versionadded added (duh) a short time after the code changes. I don’t know if the introduction of ABI flags ought to be documented more prominently; Doc/using seems still accurate, and Doc/distutils is rather vague about extensions, so I guess we’re good.
PEP 3147 modified a handful of files in Doc; I’ve added missing directives in r87312.
__cached__ is only described in library/runpy.rst and c-api/import.rst. If there is one canonical place to define what a module is (I couldn’t tell from http://docs.python.org/dev/genindex-M), I think it should be mentioned there. Copy-pasting the paragraph about __cached__ from the PEP would suffice.
Both PEPs are well covered in whatsnew. Three cheers for Raymond!