J.K. is a very shrewd operator. I would imagine her contracts with Universal look like this:
$6m (if the 6m figure is indeed correct) for PHASE 1 of WWoHP (films 1-4).
10%-20% of all food and beverage sold within designated WWoHP outlets.
10%-20% of all official Wizarding World of Harry Potter merchandise, regardless of where it's sold* (could be inside WWoHP, Port of Entry, CityWalk, online**, etc.).
Equal creative control and total power of veto over WWoHP and everything in it.
A further minimum baseline of $6m (I agree, seems way too low) for any and every future phase of WWoHP - with identical or I daresay improved % on all terms listed above.***
* Remember, Warner Brothers Pictures will also have % cuts on assorted merchandise, seeing as they own the film rights on which WWoHP is based (I believe the ONLY THING in the entire WWoHP that JK doesn't get a cut from are the DVDs on sale in Filch's Emporium, as she famously doesn't get a penny from Warner Home Video releases).
** Possibly slightly less % for online sales
*** With the success of PHASE 1, it is obvious to presume that PHASE 2 will cost Universal more in terms of the sacrifice they make with % cuts to JK and Warner. In fact I bet they are still negitoating it all now. It may also be why PHASE 2 takes much longer to realise than we would all ideally like.