@longknowledge,
I am reminded of a saying 'to be is to be related'. I think this is Buddhist in essence. Buddhism rejects the idea of substance, of anything which is self-existent, that is, existing in its own right or independently of causes and conditions.
Also this 'classical Greek' understanding you are referring to - actually I think this refers to Democritus, does it not? 'All that exists are atoms and the void' In this ontology, atoms are truly existent and all that changes is due to the changing relationships of elementary particles. Of course, this has been and continues to be an immensely influential idea.
But I agree that this ontology you are proposing is more like Heraclitus, a dynamic becoming rather than being.