How do I get the flaky top on ooey gooey butter bars?
With the recipe you mentioned there is no indication as to what temperature the cream cheese and butter should be at and I'm guessing that's one possible item making the difference.  Since it looks a little like a creaming or foaming (sponge) method for whipping ingredients, I'd try to make sure my butter, eggs, and cream cheese, but especially butter, were around 70 degrees F.  You want them to be able to incorporate air.  The first link talks about how to get things crispier or fluffier based on how long you cream, etc.  Then you will want to play around with batter temperature when it hits the oven.  

Also note that more fat in a cookie recipe, at least, is equivalent to crispier.  Are you subbing nuefchatel cheese or low fat or no fat cream cheese for the cream cheese?  If so, don't.  Moisture in sugar has an impact so make sure you aren't subbing any other sugar for powdered.

Real gooey butter cake is a yeast cake rather than the rip-off versions that use cake mix and not really all that much more complicated, although more time consuming.  You may want to try doing a more authentic recipe, or at least one that uses a yeast cake.  I have had success with the one linked.