I can patent a method of using IRC to arrange the delivery of baked goods and that would be a valid patent (actually, it's probably already patented).
No idea whether it would be valid legally because the patent office is out with the fairies but it shouldn't be valid. That's just a particular instance of the use of IRC which is a general purpose communication medium. Because it is a general purpose communication medium no patent for a specific instance of that communication should be possible. An "instance of" relation not a "use of" relation. An "instance of" relation should never be patentable because there is always prior art.
The patent office, and you to some degree, seem to be confused about the difference between words and ideas (is a file system a database?), whether ideas are the same and different (are two shades of the color orange the same or different?) and whether one idea is contained by another (is using a car to move something different from using a vehicle to move something?). The patent office doesn't seem to understand even simple concepts like Venn diagrams and the fact that words and meanings have varying overlaps and relationships. Specifically, patenting something simply because somebody has renamed and reduced the coverage of an existing concept should not be possible.
Every new patent is a new law; another opportunity for a lawyer to make money at the expense of the wider community.