I imagine they did, but Lodsys hope to convince a judge that the wording chosen doesn’t say what everyone else on the entire planet thinks it says.
Why else would Lodsys be working so hard to keep Apple out of the lawsuits? They don’t want to have this debate with Apple’s lawyers, they want to have this debate with whomever the small ISVs can afford. If this lawsuit was in “good faith,” they’d welcome Apple to the party. If they had the law on their side, Apple would have no choice other than allow their ISVs to be raped or pay Lodsys a shakedown fee to stop suing the ISVs.
From what I can tell, Apple didn't get its license from Lodsys. It's possible that Lodsys doesn't even know what Apple's license consists of, and thus the requests for discovery. I think it looks like Webvention screwed Lodsys over, selling them a patent without informing them that all the good targets have been licensed already. When this hit everyone was wondering why Apple wouldn't get coverage for their developers locked down. It seems they did, but no one told Lodsys.
No they didn’t get their license from Apple, but that doesn’t mean Webvention screwed Lodsys over. I suspect that Lodsys have an odious but well-understood plan to troll companies that are thought to infringe, but saw this as a fairly low-risk opportunity to try for a big windfall. I think they’re hoping for some hush money from Apple, but if they don’t get it they’ll go after smaller fish that haven’t played the shakedown game with Intellectual Ventures.
For example, if someone gives away free software for some kind of Open Source store on Linux with whatever it is they think infringes their patents, they’ll go after all the developers who use it, and there’ll be no umbrella licensee to intervene.