@Hp123, you keep mentioning OTE and Salary and Wages. That is about superannuation guarantee, not PAYG withholding.
Those rules are very different from the rules for PAYG Withholding. The term "salary and wages" is used in many ways, to mean different things, depending on the context.
Paragraph 12 is about defining the brackets for the rates. It clarifies salary excluding allowances. It doesn’t list all of the explicit things that aren't included. I already answered that overtime is definitely not a consideration for the "salary" brackets for travel allowances. Definitely not!
Consistency and equity is important in payments to employees. You have identified different treatment across different teams.
You can see the ATO guidance about PAYG withholding treatment for travel allowances and I've explained that if an employer pays higher than the reasonable rates determined by the ATO, the amount that exceeds the reasonable rate is taxed and the entire amount must be reported as income by the employer in STP. Employees would have to claim deductions in their tax return for their business travel expenses. If your employer is not following the ATO requirements for tax, super and reporting, ATO has a process you can follow.
I've also explained that the ATO sets requirements for how to treat a payment for tax, super and reporting. It doesn’t determine how much to pay. Does your employer have a travel policy that sets out the details about how much they pay? Are the payments processed by the same payroll team? How do they explain the discrepancy?
Deanne