Words have meanings and reflect deeper structures of thought. There can be no meditation without a self meditating. Who meditates if not an entity? Unless I am talking to a machine or a god, the entity meditating is in your case a physical and mental entity, called a person, which places him or herself in a certain mental and physical state of meditation, and then gets out of that state when it's time for dinner or to write about it on A2K...
Failure to understand or perceive something well is not a proof of its inexistence. Meditation may have its limits when it come to understanding oneself, for instence. As I see it, it's more a way to stop
the self, forget about it all and unwind, than a way to understand anything deeply or intimately, let alone the self it stopped. It's a way to spread out. One can go "beyond oneself" for a while, and then recollect oneself.
I mean, you have one central interconnected nervous system, which means whatever magic that system does has to be interconnected and systemic. the self is certainly made of parts (everything is) but connected and structured in one whole.