First, I have to fill in a form and confirm an e-mail subscription before I can download the PDF. For reference, the real download link is https://flaviocopes.nyc3.digitaloceanspaces.com/linux-comman...
Secondly, "No one can dictate which apps you can run, or “call home” with apps that track you, your position, and more."
Everything from ubuntu's amazon lens integration to android to firefox' pocket integration comes to mind. Yes, technically you can rebuild all these things from source and strip out the parts you don't like - don't like google tracking you? Chromium is open source, just edit the tracking out and build your own!
Practically speaking just about no-one can manage that. You have to either live with what you're offered or go to a lot of effort and practically have a degree in CS or equivalent. The author here has a very simplistic view of the world.
This sounds like a moderate-at-best quality article written to farm newsletter subscriptions. Could be better.