Answer
Unused Alternative Holidays should be checked before finalising a termination pay. Open Leave Entitlement Adjustments or the pay's Leave Balances screen and review the Alternative Holiday balance.
The termination form includes an Alternative holidays payout amount. Lightning Payroll values it from relevant daily pay; average daily pay is not modelled. To override the calculated value, tick Enter leave amounts manually, which enables manual entry for annual and alternative holidays together.
Do not remove Alternative Holiday days by deleting historical adjustments unless the entitlement was recorded in error. The final pay should explain the payout.