He says his problem with cell phones is that they can be used for surveillance. Later in the article he talks about how free software in the phone could protect you from eavesdropping (not surveillance). He is correct. If everything was encrypted, eavesdropping would be impossible. But they could still track your position.

So, unless I'm misreading things, he never says that the issue with surveillance is about "whether or not the software in the phone is 'free'".