I agree that the integer factorization is a poor choice. Last statement in the Abstract talks about sampling and optimization which could be the bigger point.
Their pre-processing seems like simply expanding out their cost function that's of the form E= (F - XY)^2. Of course it's a lot of multiplications since X and Y are binary and multi-dimensional. Not sure if it would be NP-hard though.
x = rand() % 2 always gives a random number. You can't
correlate them that way.
Needs to be a tunable random number and technically needs to be "true" as mentioned.
But I don't think that the authors would disagree with your larger point - their point is to provide polynomial speed-up over digital computers for a certain class of problems. That this can be done with classical computers isn't exactly a deep insight, it's rather obvious.