The EFF is on the right side of the law the same way a lawyer for a criminal is. The lawyer (eff) is fulfilling a necessary function of the judicial system even when the party they are representing is in the wrong.
The EFF has a keen interest in this case because the publishers will be doubt use this case to push for copyright maximalist interpretations of the law, and letting those interpretations become case law unchallenged is bad for society.
Edit: At a glance the vid angel lawsuit you quote is about circumventing DRM, something that is not relevant to this case since the physical books they scan have no DRM.