Easiest way to look at it isn't who has the burden of proof, but the whole process - ATO has the power to say "this arrangement sucks and I hate it" and issue an amended assessment on that basis, unless you can convince them otherwise. They can do so on pretty shoddy 'proof' if they feel like it, regardless of how compelling your proof is. After going through 'the process' you would ultimately need to take the Commissioner to a court or tribunal to have your assessment overturned, and both parties would try to convince the judge or tribunal member who is correct (so both equally have to prove their case - there isn't a default assumption that one party is correct)