We must be careful that we do not mistake artifacts of the tools we use to investigate ontology with the ontology itself. For example, we all understand now how the Ptolemaic model of the universe was us projecting our egos outward on Nature and inventing epicycles to explain things so that we remained at the center of everything, which remained true until someone had enough data to prove a more elegant theory, wherein we were no longer at the center and all the colorful drama that developed around accepting this truth.
In another example, Boolean logic, which pervades language at such a deep level that we learn to "see" the world this way by the time we have acquired language, is dependent on the abstract concept of excluded middle (which was invented to strengthen Aristotle's proposition that all statements are either true or false, not because there was any evidence of excluded middles anywhere). I see the advent of Western culture as the advent of binary logic, and thus it's hard to find a place where its implicit "digitalization" of everything hasn't invaded.
In short, the idea of things being separate from things (i.e. digital) is embedded in language at a level beneath ordinary conscious awareness -- within language itself -- and thus we don't even realize we're projecting a binary way of seeing onto Nature which is not in Nature herself. Digital ontology therefore may simply be us projecting our way of seeing excluded middles onto an analog reality and coming back with digitalness.
I believe underlying the myriad manifestations of the natural world is a singularity which operates beyond spacetime and matterenergy*. The more deeply we study these binaries, the more we find they are, one by one, merging into a singularity which operates in ways our language is not yet qualified to speak, because of its implicitly digital nature. We must develop a logically polyvalent language in order to understand reality as it is, or else keep projecting digitality onto it. The concept of superposition from quantum physics is a prime example of something non-binary which we do not yet understand on its own terms.
*and possibly beyond cause/effect, too, if David Hawkins' quantum physics can be extracted from his spiritual claims, but this one is new and still speculative to me...
The title of the following article is "Against digital ontology." It's headed in the right direction (beyond digital ontology), but perhaps it should be framed as "For informational ontology" since the for/against structure is digital/binary in nature.
https://link.springer.com/article/10.1007/s11229-008-9334-6