I had reason to pay a contractor with WT code a tax free allowance (this was actually a way for me to to address the problem of being unable to pay a GST registered contractor on WT code through payroll). I wanted the addition to be calculated at the rate of 15% of the gross pay. The addition would only calculate the 15% on the net pay (i.e. gross less withholding tax). I had to counter this by setting the addition rate to 18.75%. The resolution to this problem is to have the choice to allow additions to be calculated on either gross or net pay. I would have thought it would be quite common to want to calculate additions on gross pay.
Bit confused by your explanation above ... So are you processing it via a Supplier payment (Bills/Write Chq) or through Payroll?
Contractors don't generally receive Allowances (& certainly not tax-free ones) as these are payroll-related. If a Contractor isn't GST-registered but you still need to be paying Super for them, paying them via non-STP reporting Payroll is a great workaround. However, if they are GST-Registered, there's no capacity in Payroll to reflect this because GST is N/A in Payroll.
If paying the Contractor via Suppliers, you can add any applicable additional/Super line(s) & enter the multiply (asterisk *) symbol & percentage (eg "*0.10%") in the amount column & it will automatically calculate this for you.
To calculate on a gross (GST-inclusive) amount, just ensure the Amounts include tax checkbox at the bottom of the Bill/Chq window is ticked.