Applying for a patent is a negotiation process in which you throw out a bunch of claims looking to get the best deal you can. You start with Claim 1 being a claim on the sidereal universe and all it contains and work your way down to more specific stuff. Depending on the skill of those writing the patent you will get more or less of the invention you actually wanted.
As you can see in the application they have already dropped the first 154 claims in the original application.
And that is the main problem. When an inventor files a patent, it should be totally specific. If that patent is rejected, they should have two options: Argue that the patent as it stands is valid, involving the courts if necessary, or toss it out, and create a new, correct patent with a new effective date.
And if the way a patent is written could be read to cover some prior art, either before or after it is approved, then the patent is wrong and should be tossed, entirely, unless that prior art was explicitly listed in the 'prior art' section.
So this patent application should be the recipient of a junior-clerk's REJECTED stamp, because it doesn't explicitly list the Satoshi paper in it's applicable prior art section.