I'm confused discounts / reward points / shipping cost (answer for my self)

Hi!

I get confused about the work of payment calculation:

The order subtotal is $1,700.00 the paymentMethodAdditionalFee is 3%, then $51.00

1. If I select a shipping method of $14.70 the paymentAdditionalFee go to $51.44 (0.86% increased) . If  I select Pickup in the store of $0,00 the additionalFee stay in $51.00

2. In the same additionaFee if I select the "use my reward points" and the reward points amount is $75.00
paymentAdditionalFee go to $48.75 (4.41% decreased).

If have a discount of 5% and is over order subtotal, when customer has spent $1,000.00  then the discount is $85.00

3. If the order have the discount the additionalFee go to $48.45 still when no reward point or pick up in the store is selected.

Sumary:

If I select a shipping method with value > 0.00 the additionalFee is increased.
If I have a discount or select "use my reward points" the additionalFee is decreased.

Question: If additional fee is over the order total why it have the amount changed if I use the reward points, discount or shipping method?

I answer for my self: sure if the additionalFee is over the order total and I select a shipping method with amount > 0.00 the order subtotal + shipping cost will increase the additionalFee amount.
And in the second the discount is over the order subtotal then the additional fee is over order total which has decreased by discount and reward points.

Forgive me if I can't understand a few basic things why I am a newbie (it's a shame, question before think about).