1) The abstract appears to be an opinion piece; I don't know how they do things in philosophical journals but I would hope for a dryer standard.
2) Nature is really messy - it'd make sense if parts of our bodys were actually parasites. The immune system, gut flora, skin mites are all obvious places where foreign hostile bodies might colonise then integrate into humanity over time. If an addition has any benefits evolutionary pressure will eventually cause it to become symbiotic.
3) Humans are by design easy to manipulate. We're social animals built to group up behind leaders and do what they say. There are brutal social hierarchies where low status humans live relatively unpleasant lives because high-status humans think that is reasonable. We're not built to unthinkingly optimise out own personal outcomes of make all the decisions ourselves. Humans being manipulated is not, in and of itself, a hint that things are going wrong.
4) "It is not plausible for a part of the cognitive system to be designed to thwart the goals and desires of the user in the way a smartphone is" - it absolutely is, the #1 enemy of most people is their own mind. It leads them to do wildly stupid things. There are people who spend their entire lives working to overcome their own cognitive systems to achieve peace and happiness.