Good essay. Emergent Integers indeed! Can't help but notice that your view is decidedly not Pythagorean! I disagree: math IS reality. Whether this is a Virtual Reality or no that I am typing this comment in, there can be little doubt that if this is virtual, then reality is digital. If it isn't, nevertheless your DNA (the code that programs life--is).
If we were to program a simulated Reality which would be indistinguishable from this one (the one we agree is Objectively Real), we would simplify the code to a few mathematical equations (e.g. Gravity the other three forces). Then we would transform those laws into the code of our programmed reality.
'Many years later', or iterations, the inhabitants of the virtual reality would develop sophisticated experiments and methods to discover the underlying mathematics governing their reality. Ultimately, they would begin to question then why the math is what it is. They would form hypotheses about Virtual Realities and Hidden Dimensions and Utimate Multiverses. All in an attempt to shy away from the suspected Truth: they are programs in a Virtual World. Or that God did it. Such has Science come to be: a strident clarion-call that everthing is godless (but nevertheless beautiful and true and elegant). It's time to capitulate, and begin to accept a melding of Religion and Science as we move forward. And harken back to making Aristotle's MetaPhysiks rigourous.
Eh, what am I doing in here anyway; shouting in dark? Oh yeah almost forgot: it is my conclusion that the VR Hypothesis is no Hypothesis at all, and all this various verbiage of mine is an attempt to be exceptional in this Reality. To try to stand out and get the programmer to notice me. Oh, and incidentally, to try to convince someone to offer me a job or a Grant so some serious attention can be paid to this perhaps most important of topics by this point-like wave-ish program who imagines himself an Author...
And to become what Destiny demands: Doctor (Ph.D) Witch Doctor. Has a better resonance than merely witch dr., no?