4) making someone aware and giving them the opportunity to cease and desist from commercial infringing activity
Is that a threat?
It's one thing to tolerate infringement from a community open-source project. It's another thing to let someone commercialize that technology and bundle it with hardware when a fully proprietary competitor would reasonably expect to be sued in to bankruptcy in no time flat. Should the fact that part of your business is "open" give the whole business immunity from patent infringement claims?
Also, IBM isn't "a self-declared friend and protector of open source". They only made a limited non-aggression pledge. They aren't (and aren't trying to be) in the same category as the FSF and EFF, or even RedHat.