I noticed this test in package-document.feature refers to issue #522 for making it a warning:

  Scenario: default vocabularies must not be assigned a prefix
  	Note: This should be an error, but is currently reported as a warning
  	See issue 522: https://github.com/w3c/epubcheck/issues/522
    When checking file 'property-prefix-declaration-default-vocabs-error.opf'

Issue 522 is about reserved prefixes, not reserved vocabulary URLs. You may declare reserved prefixes, but that's separate from trying to assign a prefix to a default vocabulary URL.

So the note is right that it should be an error. No reason I can find why not.