Logic of Emptiness still unconvincing. Please help explain

I've been a practitioner of Vipassana and Mahamudra for 2 years now. One thing quite bothering me is various explanations from different teachers on emptiness logically disturbing... Usually, it goes like this: > The flower before you seems real. Now get closer, you no longer see flower, but just leaves, stem. Even closer, you "see" atoms, electrons, etc. See? the flower is "empty" of inherent existence. The same goes for "self". Try search for the "self" in your thoughts, arm, leg, etc. and you would find nothing. Of course I could appreciate this mentally helps in someway in practice. But something falls short. First, it feels "outdated" to me, in a post-calculus world, that it denies the validity of an aggregate object, by pointing towards an infinitesimally small part of it. Zeno paradox? Secondly, the requirement of "look closer" (or farther) seem to assert the perceiver model. That logic (or its inverse) would seem to imply that, "in order for something A to be *truly existent*, that thing needs to be A in all perceivable cases". That A would then seem to be only possible as some kind of "totality", or awareness itself. So that felt like a semantics game then. I'm sure there're better ways to explain the Buddhist emptiness logic in a more modern compatible way. Please enlighten me.