With the establishment of the commission, the secretariat would be a stand-alone department. When the commission was established, first of all administratively, by order in council, the secretariat was established as a full-blown, stand-alone independent department, exactly for the reasons you mentioned, namely, to ensure that support for the commission comes from its own entity and not from a secretariat attached to any other entity.
Because the creation of the commission is in abeyance, for administrative purposes the secretariat is functioning within PCO, in the sense that there's an agreement for shared corporate services. It made no sense in such a small entity to establish an HR shop, an access to information shop, etc.
There's such an arrangement with PCO for administrative services. But the way it would be established by order in council would be for the secretariat to be an independent stand-alone department. It would continue under a commission established under the Federal Accountability Act.