The ATO have confirmed (and now published current process and instructions on their website)
ATO Website instruction
Please refer any discussion with the ATO call centre to this page. Specifically th FAQ section that states as follows
Do registered agents have the authority to complete the notification on behalf of their client?
Yes. The agent can do the SSID notification on behalf of the employer regardless of whether they will be processing payroll/lodging the pay events.
The SSID registered, must be for the party that will be lodging. If they think that both the agent and/or the employer may lodge at different times, there is the ability to register multiple SSIDs (i.e. the employers and the agents SSID).