I don't think I'm confusing the two, I'm saying the connotation is what's important when the connotation is what is almost always used.

Unfortunately, this sentence itself seems to betray some confusion: "connotation" is not a kind of alternative definition; hence it makes no sense to say that "the connotation is what is almost always used". Rather, both denotation and connotation are always present whenever a word is used. "Connotation" refers to implications a word has outside of its meaning. For example, the words "copulate" and "fuck" have the same meaning (denotation), but differing connotations.

The crucial difference is that, while changing the denotation of a word (or getting it wrong) can change the truth-value of a statement, merely changing the connotation never can. Instead, it merely changes the register, signaling-value, or "appropriateness" of the statement. A scientist, in the ordinary course of affairs, might report having observed two lizards copulating; but it would be rather shocking to read in a scientific paper about lizards fucking, and one virtually never does. However, if a scientist ever were to write such a thing, the complaint would not be that they had claimed something false; it would be merely that they had made an inappropriate choice of language.

A lot of verbal humor results from using "inappropriate" connotations. The "edible" quote is an example of this, in fact. The listener understands that the sentence is true but still "off" in some way. Using an inappropriate connotation is not a misuse of the word, otherwise the humor wouldn't work (or at least, it wouldn't work in the same way -- there are other forms of verbal humor which do involve incorrect usage).

And I'm not claiming that the quote is wrong, just that it's not really a rationality quote

Well, I agree about that -- but that doesn't really seem to have been the main thrust of your comment. Your claim seemed to be that the quotee had redefined the word "edible"; and this is what I am disputing.