For STP INB Payee Gross Payments [PAYEVNTEMP47] the ATO states “Do not include amounts that have been salary sacrificed.”
So the STP amount is gross taxable.
Using your example report:
$388.50 for STP INB
$611.50 for RFBA
There is another field called OTE Amount [PAYEVNTEMP61] this would be $1,000.00 because this is used to ensure the employees super is being calculated and paid correct, which is field Reportable Employer Super Contribution [PAYEVNTEMP111].
Hopefully your payroll software will be able to automate this pretty easily.