Hi Genreve,
I have a similar issue. Need to submit an STP finalisation for the 23/24 year. I also have spoken with ATO and given them the same information that you have provided and received the same response as LizS288. The ATO simply had no idea how else to do the finalisation and I was transferred to several different staff members at various levels and various departments. If you have a contact at the ATO that knows what you're talking about, we'd love for you to pass this on.
In the meantime, I am signing up for an alternative Payroll provider who can do this.