I think there maybe some confusion as to what part of the setup costs can be reimbursed. I believe Eric and the reference to the ATO are referring to the trustee set up costs and not the super fund. Reimbursement for the super fund is no problem, but is the trustee part of the super fund?
Whether right or wrong the ATO have made the statement the corporate trustee ASIC fees are not deductible to the fund, and not payable by the fund. The logical extension from this is the setup of the corporate trustee is not an expense of the super fund.
Remember a super fund is just a trust, so requires a trustee, but that does not mean the trustee and the super fund are joined at the hip, both entities are separate under tax law.
Do I agree with the ATO, possibly! I think if the corporate trustee is a special company you have an argument to say they are linked. But if the corporate trustee is set up as an ordinary company then how do you treat the company with regard to the super fund? The ATO may be correct in its interpretation.
I hate to say it but again it may come back to the fund trust deed, sometimes we forget how important the wording of a trust deed can be. Whether the ATO or APRA say something is deductible or can be reimbursed may be immaterial if the deed does not allow it.