Hi there,
Thanks for this suggestion.

To avoid small overage fees, I'd suggest selecting the Overage Billing Charges option which adds the fee to the client's next service renewal invoice: https://docs.whmcs.com/Automation_Settings#Overage_Billing_Charges

If the separate invoice is required for overage changes, would limiting auto-captures be the best solution for optimising transaction fees? If the invoice is not auto-captured, wouldn't the client just pay it manually, thereby accruing the same transaction fee anyway?

Perhaps a feature request to waive overages below a certain threshold, or accrue them as Billable Items until a certain threshold is reached before invoicing separately, would meet the need here?