From the alliance website:

"In light of these early, important licensing endorsements by Intel and AMD, the market demanded greater clarity and certainty...........

The MMP Portfolio Licensing Program therefore focuses licensing requirements and royalty collection on the finished "system-level" product. A royalty-free MMP Portfolio license is also available to manufacturers of chips and other unfinished goods.

It seems they are saying there are two types of licenses, and if they stated such in their original contracts to Intel and AMD then they could indeed double dip. I believe the case that you are referring to, the Supreme Courts decision, even stated that had LG made such specific conditions in their contract then it would be allowed, but they hadn't. What we need to determine is whether TPL and Patriot had that kind of wording in their contracts to Intel and AMD.

Regardless of what they did with Intel and AMD any future manufacturers will have that condition in their licensing agreements. The manufacturers can either bear the cost of the entire industry segment, or purchase a manufacturing license and let the system manufacturers ( the Dells etc) pay as they go. As long as the intent is specific it would not conflict with Quanta vs LG decision.