"so while its informational content may be ~3 billion letters, those letters can and are part of a dynamical system when encoded in DNA. I'm not sure if what this means in regards to its total informational content."

It means nothing, in terms of information content.

This is a common misunderstanding, which the author of the piece appears to share, but there's no getting "more" information out of something by talking about its interactions. Suppose we write a computer language where every byte is a meaningful opcode, and all possible strings of bytes are valid and do something. If we consider the set of 8-byte programs, there are 2^64 of them. It takes 64 bits to encode which one you are choosing from that set, and there are 2^64 options. The fact the they are "programs" and thus that many of them will "interact" does not mean that you suddenly have more than 64 bits of information. You still have just 2^64 options. None have appeared from the ether by the virtue of some of them "interacting". In that set of programs will be everything from programs that immediately terminate, to infinite loops, to programs that use staggering amounts of RAM and CPU before terminating, but there's just 2^64 of them.

Information is really just a count of possibilities. (Weighted, technically, but that's not a terribly helpful detail at the moment.)

Since the question is explicitly does DNA itself encode innate knowledge, it is relevant to discuss the contents of the DNA in this strict counting argument. (Add the epigenetics and whatever else you like; all it does is add more bits proportionally to the possibilities they add. But they don't make more bits than that due to "interactions".)

You, yourself, are not the sum total of information in your DNA. Even at the one-cell beginning of your life that would be an oversimplification, and since then the universe has poured far, far, far more "bits of information" through you than you could possibly have integrated into yourself. You would require a great deal more information to describe than your raw genome (just as identical twins are still, you know, distinct people). But in terms of asking what can be in the DNA alone, the information theory is relevant, and citing "interactions" buys nothing. The DNA has the bits the DNA has and it doesn't get any more by "interactions".

The organism with the DNA will interact with its environment, of course, and it's essentially proved that a lot of our "innate knowledge" requires interacting with the environment to develop. In terms of understanding the whole process, that will all be critical to understand. But in terms of literally what is in the DNA, that's not particularly relevant.

(My personal belief is that a non-trivial component of the confusion is indeed that we look at the "final product" of this innate knowledge and over-attribute it to DNA. Babies naturally recognize faces... except they don't. "Face recognition" is a huge amount of bits. On the other hand, encoding some instructions that will result in embedding an eigenface [1] into the visual system and giving a hint of dopamine when it recognizes one, and leaving the baby to eventually work out what "faces" are and why they are interesting isn't that many bits at all. The end result is "face recognition" and that system would consist of a huge number of bits' worth of information, but the vast bulk would be from the environment. What was actually in the DNA is just a tiny seed crystal of information, which fits perfectly comfortably in the DNA. Especially since it wouldn't even necessarily be a "thing that matches faces" but just a weird streak through the hyperspace of possible visual inputs that happen to privilege faces but will also privilege and disfavor any number of other inputs too, which reduces the requisite bits even further since we don't have to "spend bits" on truly selecting on "faces". A lot of our "innate knowledge" doesn't really take that many "bits" in the DNA.)

[1]: https://en.wikipedia.org/wiki/Eigenface - note even the samples the Wiki gives are more complicated and information-rich than would be necessary for the scheme I describe to work.