Based on Adobe's announcements on this subject earlier in the week, the licensing requirement only applies to apps that use
both the 3d and memory-optimization technologies. Using one or the other by itself won't require licensing. The practical effect on Unity-Flash games are that small 3d games should not be subject to the licensing requirement.
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).