>2. If the answer to #1 is yes, how does Apple avoid this problem? Are they also licensing from Microsoft? Or is Apple in some sort of a mutual cross-licensing agreement here to fight the common enemy Google?
They are all in a sort of standoff, as they cannot sue each other without putting themselves at risk of counter-claims. In addition, there are a number of cross-licensing deals between various large patent-owning entities, as you correctly surmised. Microsoft found a way around these issues, by suing Android implementers (such as Samsung, HTC, etc.), who do not have such large patent portfolios with which to make a "second strike".