The EFF is an advocacy organization. It definitely "advocates", and does not generally make "rational" arguments. If you always like everything they do, you may have a hard time seeing this, but if you've ever seen them speak about something you are either ambivalent about (probably a lot of people on this matter today) or even outright disagree with them on (as I have), it becomes clear.
I'm not particularly trying to be critical of them here. They advocate; it's what they say they do, it's what they are set up to do, and they're generally in a space that nobody else is even close to advocating for. But I do think it's important to understand them for what they are.