Re: So how were they making money?
My understanding is that they applied the usual modern financial business approach of creating unnecessary financial transactions between unnecessarily complex arrangement of companies, which muddied the waters enough so the ATO couldn't work out how much was due or which entity was responsible for the income tax payments.
Stealing employee's superannuation contributions is rife in Australia, and most of the time the employee cops the hit and is not reimbursed. This is building up into a budget timebomb for 2030 and beyond because of the compounding effect of reduced superannuation savings.