ORDER BY, LIMIT/OFFSET have to do with presentation of data. So, although it's highly desired that a language based on the relational model supports them, they have nothing to do with the model per se.
As for opaque keys, I thought the old debate about surrogate/artificial and natural keys was over years ago. The relational model has nothing to say about it, that would be like trying to make a model understand if facts are true in the real world or not. A key is a key.
Moreover, last time I've checked transitive closure operators were defined for the relation model (people should not stop ad Codd papers, Date and Darwen wrote a lot of books, e.g. The Third Manifesto, extending on the original ideas).
NULL is a completely different beast and this is the only real thing one can consider problematic.
In some cases NULL just means the predicate for the relation is different because values for an attribute don't apply, so this is not really a problem, in some other cases we simply don't know the value when we are collecting information, and this is indeed a problem.
Date follows Wittgestein that said we should remain silent about things we can't speak about i.e. we shouldn't collect incomplete information, Codd came up with I-marks, A-marks and n-valued logic, SQL collapsed everything into NULLs and 3-valued logic.