(1) What if an agent asks for a partial and is then closed to queries when the manuscript is ready?
(2) Or what if the instructions to submit a referral go against the agency submission instructions?
(3) In a word, what happens when you get varied instructions for the same task, and aren't sure which path to follow?
(1) Send the partial. You're not cold querying when you're responding to a request for more material.
(2) Do what the agent told you. The published guidelines on the website are more general than the specific instructions an agent gives you directly.
(3) Always do what the agent tells you. In the absence of specific, individual (or in-person like a class) instructions, follow what the website says.