I think what you're missing (if anything at all) is that Hoffman is playing word games.
Reality and perception are heavily overloaded words. For example, you interpret perception in terms of excitations from spectral stimuli. For Hoffman's theories to make sense (i.e. applying the Principle of Charity), we need to define perception in terms of a mental model of the cause+effect relationship among physical things.
Both of are you admitting that our modes of perception discard relevant information, which could cause us to make wrong deductions. But we need Hoffman's more encompassing definition to allow us to say that perception is intrinsically and irredeemably at odds with reality. The problem is that were he strictly correct, Hoffman would never be able to make the statement in the first place. The false reality isn't absolute if you can deduce that there exists another reality. And like with cryptography, that little chink in the armor plus applied logic is often all you need to tear down the wall.
Clearly humans are capable of seeing past the immediate false realities our brains construct, permitting us to examine indirect realities (which may or may not be the same thing as "objective reality", whatever that's supposed to mean). Which suggests that there isn't a single "reality" that we perceive as humans; there are different levels and dimensions of perception and "reality" which we could identify with similar rigor, and clearly Hoffman's assertion cannot apply to them all equally. And the assertions are obvious trivialities if he's referring to the basic mental models we construct in our daily lives.
To put it more concretely, science and math allow us to see past our immediate physical senses and mental modeling, at least in so far as they allow us to make predictions which we can and do subsequently verify. That much is clear, and that destroys Hoffman's argument in as much as it relies on handwaving about genetics and evolution. The rest of the argument would appear to just rest on ground well trodden by various philosophies of epistemology, semiotics, etc. And that's a quagmire I'd personally prefer to stay clear of because it's not at all clear we understand what the relevant questions are.
I never studied semiotics, but I think we could all do better to keep in mind that words are funny things, and just like the way we perceive physical reality, we tend to subconsciously fill in the gaps (or assume they're filled in) to construct reasonable interpretations of theories. Reading summaries of Hoffman's ideas my first thought was that he's relying on special definitions of overloaded words. Which suggests 1) his theory, if sound, only makes sense within his unique conceptual framework and thus the conclusions don't mean what they superficially mean, and 2) there are a lot of obscured, hidden premises that are either wrong or speculative.
Pedantism is a virtue, not a vice. When someone says that being overly pedantic is not constructive, my first thought that is that 1) yes, that's a good assessment, but 2) if it's possible to be overly pedantic (but still reasonable) then the fact it's being unproductive is more a reflection of a lack of substance in a discussion. If people can point at meaningful problems with interpretation of words and phrases, that suggests the discussion is built on sand. Similarly, unless a hypothesis is testable and falsifiable, people should put little stock into it. Hoffman's notions are so abstract (literally, semantically) that my instinct is to turn and run. Which isn't to say he might not be on to something, but untangling the mess is probably more effort than discovering anew whatever useful insight lay beneath it all.