So the conclusion to this little sage is that once I escalated my complaint Beem offered to pay me the $2,000 with my agreement that I would repay it once the payment showed up, which I accepted.
I did ask them to send me the Bpay reference number etc so I could follow up with the ATO and see if I could expedite things but they didn't respond to that. It seems they dealt with the ATO in the background and the payment has now been credited to my ATO account with a "processed date" 30 days after the "effective date".
I have now repaid the $2,000 to Beem so it is all now sorted.
Not a great thing to happen but it worked out in the end, although it did take some time and about 15 emails back and forth to get it resolved. I give Beem credit for managing it well once I got past the first-level support.