Puka is and always has been the easiest franchise tag decision in league history. His salary would be more, he's had injuries and off the field issues. So I'm not worried about the contract. This just makes that an easier decision.
As for recovery, what I can find online is that an MCL and PCL sprain usually takes 4-6 weeks. IR will make him miss 5 (including the bye), and I wonder if that's why it wasn't a guarantee that we would place him on IR (Sean said "likely to")....if it ends up being the lower end, he could in theory be ready against the Niners, whereas placing him on IR means he would have to miss that game.