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Discounts factoring into payment calculation default application when rule is set to proration?

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Discounts factoring into payment calculation default application when rule is set to proration?

 What is the problem?
How do discounts factor into the payment application calculation when your default application rule is set to Proration? In my scenario, there is one discounted line on the invoice and when I apply a payment for the full amount the discounted line is getting overpaid while the non discounted lines are getting underpaid.

The proration rule will skip all the non-positive values and this is the current designed application behavior.  The function is worked as we designed. 
Issue reported by customer

The customer has an invoice which has 3 line items: 
They've made a Payment in order to cover the Invoice Balance, however the distribution of the payment doesn't seem correct: 
The Application Rule settings are as follows when the Payment was carried out: 
There should not be any Proration happening whatsoever as you can see for yourself in the screenshot above.  
Business impact on customer
The customer is trying to pay bonuses based on the invoice payment performed on the Invoices, however since the Payments are not applied evenly, it is rather hard for them to do this.
The reason that doesn't work is because Zuora is deriving a proration value that is greater than 100% of the bill (8042.77 instead of the actual invoice and payment value of 7993.96) because they're not considering the discounted line items.  That I could've discounted 100% of that line item and Zuora stillwould've applied money against it seems totally wrong to me (and problematic for our reporting, commissions, etc.).

I would expect Zuora to at least consider the discounted amounts against the original line amounts to come up with a correct 100% total of the invoice.
Currently, the discount item New Customer Discount (16.67% for Initial Billing Term) could be counted into the line item Stack Overflow for Business Seat (Annual), where the tax item of discount could not be counted into the tax item of the invoice line item.