I enjoyed reading your stimulating essay. You distinguish between two ways the analog/digital debate can go: '...(1) as a claim about the discreteness (or not) of space, time, and matter; (2) about the computational nature of the universe.' In my own essay, I pursue the latter course.
I've taken the liberty to comment on some of your passages, in a manner I hope will be welcome:
'Often the assumed denseness of an analogical model is parasitic on the assumed dense nature of the process or object functioning as the model.' I would point out that, similarly, often the assumed "sparseness" of a digital model is assumed to reflect some ontological discreteness in nature.
'...the question "Is reality digital or analogue?" concerns representation,
and representation involves intentional systems...' The digital strikes me, specifically, as paradigmatically a product of definition. The analog is too--technically speaking (i.e. as a mathematical definition)--though through common experience it is more familiar and so is more readily associated with the natural reality it represents. That is, one thinks of the real mercury in a thermometer as 'analog', since its expansion appears macroscopically to be continuous, whereas the scaled markings are 'digital' and clearly imposed for the sake of "reading" the temperature.
"...that which we call reality arises in the last analysis from the posing of yes-no questions and the registering of equipment-evoked responses; in short, that all things physical are information-theoretic in origin and that this is a participatory universe." [Wheeler] This may be what Wheeler calls 'reality', on some phenomenological basis, but it cannot be the usual sense implied by physical realism. I would agree that this describes physical knowledge, though not necessarily physical reality. I can sympathize with the sentiment of a participatory universe, though I suspect Wheeler goes somewhere with this I would not dare to. Again, he seems to be talking about "experience" rather than "external reality".
'For Wheeler, in an important sense, epistemology precedes ontology: bit
precedes it.' However, 'bit' is a concept historically derived from 'it' (info theory from thermodynamics). Even if we consider it logically independent, it is still a concept derived from general experience in the real world (bit = thing), just as set theory is. The conclusion is recycled as the premise.
'...there is no such thing as a phenomenon until it is an observed phenomenon.' This is an ambiguous use of 'phenomenon'. It should mean EITHER the representation in experience (or in science) OR the thing it represents, but not both. Similarly in the expression '...past events are not definite'. 'Definite' is ambiguous, since it can refer to what is definitely known or what is causally determined. Wheeler should have known better. But your sympathetic conclusion is justified: 'Theories about the physical world inescapably bear our imprint; they are constructed to account for our experience.'
'All we have to go on in science... is pointer-readings, the record of some interaction, and the relationships between such entities. These take the form of coincidences [events]...' This reminds me of Keith Oatley's description (in 'Perceptions and Representations, 1978) of "flying blind"--the metaphorical position of the brain, sealed inside the skull, obliged to navigate solely by instrument. Also, Maturana and Varela pursued similar ideas ('Autopoeisis and Cognition'), generalized to the case of the organism in relation to its environment. Taking off on these concepts, I once wrote a chapter in a philosophical novelette, to explore the encapsulated brain metaphor through a Cartesian theater analogy. The protagonists somehow find themselves inside the control room of what appears to be a space ship of some sort, but turns out to be an advanced alien machine-based life form(!) They discover for themselves the art of flying blind when they try to figure out how the thing works, simply by trial and error of observing correlations between inputs (control levers) and results on their instrument displays. They then develop a program to account for these correlations, thus creating an automatic pilot and (largely) working themselves out of a job...
'All physical theories are, in this sense, approximations: they go beyond what
is observed (namely, discrete events).' I think more can be said than that they are "approximate" in a quantitative sense. There is a qualitative difference between theory and reality, which I like to characterize as the difference between artifact (the 'made') and natural reality (the 'found'). Certainly I agree that expecting too much can get us into trouble. I do think, however, that there is some utility yet to be squeezed out of recognizing this qualitative difference, and not mistaking the map for the territory.
Thanks for a well-written essay, a pleasure to read!