Dear Armin,
Thanks for reading my essay and I appreciate your comments. Your query is an intriguing one and is at the basis of 'our' epistemology. I have made it clear in my essay while concluding that 'mind can know It only through Bit although It (reality) is having an independent existence'. So the problem of knowing It apart from Bit by the mind wouldn't exist and that is why I have concluded in my essay that 'for our knowledge to exist all three (It, Bit and mind) must coexist'. Speaking in terms of physics (or, in general, in science), It is having different forms and it depends on how you cognize It by interpreting different Bits in different terms. One of the best examples is gravitation itself; you can view it in Newtonian-way, Einsteinian-way, phenomenological-way, etc. The same thing happens in the quantum world also. So as to your question "What equations in physics point to the existence of a reality apart from it or bit?" I would have to answer in the negative. In this sense I agree with your belief that the 'existence is not a binary concept'.
It is only in religions that the 'absolute reality' (usually called God) can be grasped in its 'purest' form as it is, in the 'mystic experience' and this experience is 'indescribable' in terms of language or mathematics and it can only be 'felt'. Here also the existence of 'subject' and 'object' is not a binary concept.
I look forward to hear from you more and I have down loaded your essay and soon post my comments in your thread.
All the best,
Sreenath