Microsoft is putting the possible infringers on notice, as necessary. Red Hat for example can't say "we had no idea" at some point in the future.
Yes they can. Microsoft would have to tell them exactly what it's claimed that they're infringing for the clock to start ticking. Again, all large software infringes on something, so you can't expect every software vendor to suddenly shut its doors because they have the knowledge that they may be theoretically infringing on a patent.
Software patents, especially of the poor quality of most of them, are damaging to all small software developers. They serve to make sure only the large development houses can stay in business.
Microsoft is putting the possible infringers on notice, as necessary.