"All processes that exist entirely in software are representable as a series of mathematical operations. Therefore, software methods are math"
This is where your argument breaks down. This is not logically sound.
Just because something is representable in some other form, does not mean it is that other form.
The interactions of subatomic particles can be represented by a series of feynman diagrams. It does not follow that interactions of subatomic particles are actually feynman diagrams.
If you want more examples, there are plenty of things in physics that are representable as interactions and models that are provably do not occur that way in the physical world :)
instead of "are representable by a series of mathematical operations", you want to say "are in fact, a series of mathematical operations "
Even then, the argument doesn't hold because they aren't patenting processes in software. They are patenting processes (which is valid), particular instances of which happen to be represented in software.
There are good arguments for why software patents should not exist. Most of them deal with abstractness of the processes or claims, not "mathiness".