Sorry for the late reply. With SDCC and new pre-orders around the corner, I suppose its a good time to clarify now:
Correct, when you apply reward points or any promo/discount to your order, SSC will not give you Reward Points for whatever value that may equate to. So your example is correct where you were applied $100 worth of Reward Points on a $400 figure and was awarded only Reward Points for the $300 you paid via debit/credit card or paypal.
However in the event you had paid for that remaining balance of $300 on the $400 figure via Gift Card, you would have gotten Rewards Points for the $300 Gift Card you purchased, on top of the Rewards Points that are awarded for the purchase of the figure itself.
Here is another example: Mark L is retailing for $407 currently. If you apply a $25 Marvel Promo code, you are left with a balance of $382 (excluding shipping). If you purchase a
gift card for $382 and apply it to the Mark L purchase when checking out, you will receive Reward Points for the complete value of the $382 Gift Card ($382/20 = $19.10 worth of Rewards Points), along with another $19.10 for the purchase of the Mark L itself.
So rather than getting the typical $19.10, you are earning double ($38.20) due to payment via Gift Card. This takes commitment for figures that are not yet released however, as you are essentially pre-paying SSC in full.
Enjoy, everyone (while it lasts)