I'm not sure if we are talking about the same, but MC3 is a type of lipid, which ALNY claims. The TKMR patent is a ratio and formulation of lipids, which can be with MC3, or another. If ALNY uses MC3 with a certain ratio/formulation, it needs both patents. If ALNY has a license to the ratio/formulation patent it can claim a proprietary delivery system, just like they didn't invent RNAi, but got the exclusive license.
The billions in damages is always based on winning every claim and a multiple, almost never happens.