If you aren't using the official channels for your application and have in-app purchases, will you be liable for patent infringement? ...
I am sure that if you implement the in-app purchases in your independent way, and distribute your application yourself, you also need to get the patent. But what about the third party stores?
Don't be so sure!
The biggest kick in the nuts for Lodsys in that letter is when Apple says "Lodsys's threatened claims are barred by the doctrines of patent exhaustion and first sale". As I read it: because Apple have already paid for a patent license for each iOS device that they sell, no-one can demand another license fee. It's already licensed and paid for. Lodsys is effectively asking to be paid multiple times for the same device, which they can't do.
So, assuming that Google and others are similarly licensed to Apple, Lodsys would not be entitled to any fees from apps on unofficial mods and third-party stores. That's because the Android mod or third-party apps could only run on devices which are already licensed — the mod or app might not license the patent directly, but each user of the mod or app effectively has, because Google or Apple or whoever paid their license fee to IV for the device. It could be that almost every owner of a smartphone in the world is already licensed for this patent, which would make Lodsys feel sick in the stomach (if trolls have stomachs?)
(Remember IANAL and IV got paid for the Apple license, not Lodsys, but who got paid makes no difference)