You are hinting at something important here. Let me strengthen your point: to own an object means to subject it fully to your own will. If the object can act in a way that favors someone else's interests over yours, you do not own it. This is true of pretty much any device running proprietary software.
A litmus test: can you make your device lie to the manufacturer's servers? Regardless of the legality or morality of doing so.
However this article is really about something else: the vulnerability of centralized services in the face of government oppression. Signal only has the ability to log messages because it is a centralized service that controls both the client and the server. The benefits of E2EE is greatly reduced if the client and the server is controlled by the same entity (tomorrow Signal can push out an update that would send a plaintext backup to their servers, and you wouldn't know it until later). Moreover, the non-free distribution mechanisms on mobile phones (stores) limits a company's ability to resist.