I had a hunch my email to Mark Small of Lodsys landed on the day his inbox blew up, and according to the Lodsys blog, that's exactly what happened. The patent holding company has posted a lengthy Q&A on its blog, clarifying why it sent out requests to individual developers to license its "upgrade" technology for in-app purchases and lite-to-full upgrade functionality.
According to Lodsys, Apple (as well as Google and Microsoft) already licenses the Lodsys technology for upgrading, but this licensing does not extend to third-party developers. Considering Apple only sells a handful of apps to begin with, and of those apps I'm not aware of any that offer in-app purchases (let alone a "lite" version), obviously this licensing wouldn't apply to those apps. It would, however, apply to all third-party developers like those getting notices last week.
So either Apple didn't license things properly, or the onus is really on developers to come to terms with Lodsys. It's fair enough for Lodsys to offer licensing, although I have to say their attitude in the Q&A is very defensive. At times (the remark about "pixie dust" in particular) they sound as if third party licensing isn't even possible -- which is ridiculous. Of course it is. Apparently Apple either didn't do it or there's been a misunderstanding.
Either way we'll keep an eye on things -- because this isn't going away, nor is Apple's App Store and iOS ecosystem.