Unity's export to Flash does currently require both 3D and memory-optimization technologies. Any Unity-Flash game that has a chance of netting $50k falls under the requirement, from what I currently understand. This basically covers any non-hobbyists. Unity could solve this problem by making their Flash exporter not use "domain memory", but that might be technically infeasible.
One interesting question is, if my company makes 5 games, each of which makes $49k, is that legit? Could I get away with taking down any game right before it nets the magic number and putting up a "new" game which is only slightly different? I'm guessing the answer is "no", but edge cases sound like a nightmare.
Yes, but all Unity games on Flash do use both. So all Unity games on Flash will need to pay 9%.
Caveat: Adobe has actually not issued specific rules or statements on when licensing is required, so until they do, any analysis is really just conjecture.
Edit: The facts on which I based my analysis have changed. Adobe has issued a FAQ, and Unity has confirmed that the Unity-Flash conversion uses both features. Consequently, the practical effect is that any game that succeeds in reaching the $50,000 revenue threshold will incur licensing fees of 9% on the revenue in excess of $50,000 (i.e., $0.09 for $50,001 total revenue, $4500 licensing fee for $100,000 total revenue).