Section 9 of the model Standing Orders covers the preparation of the agenda and sets out the respective roles of the Proper Officer and the Chair. If a motion is deemed improper, the Proper Officer should consult with the Chair to determine whether or not to include it in the agenda, but it is the Proper Officer who makes the final decision.
So in answer to your question, the power lies with the Clerk, but differences of opinion between Clerk and Chair should ideally be resolved by negotiation, rather than by reference to the rulebook.