This is strange. The ref:vatin should be an international standard format, which contains the country code.
I didn't have any information about this Czech specific.
I read the discussion, so I will not longer change the ref:CZ:vatin tag. To avoid misunderstandings it would be nice to create a wiki page with your information. Until this key is used more than 10 times you could add a note tag with some explanations to every features, which uses this tag.