The problem with his line of argument is that he is too used to theological thinking, in which one can bullshit to one's heart's content because it is all interpretation and nobody can prove you wrong. He seems to think this applies to all fields of academia and forgets, or doesn't want to remember, that some fields make a habit of testing their theories against reality.
He started with a perfectly valid point, in that we have no intrinsic way of knowing if our thoughts and perceptions are actually reflecting reality or if they are just biologically useful illusions. That's fine. His mistake is to extrapolate this into claiming that there is no way we can seek confirmation from reality and therefore we should rely on the silly Quran so there. That's where he fails miserably.
Also, his crack about Popper demonstrates ignorance. Popper ended up withdrawing his definition of "falsifiable" after more discussion and reflection but this is hardly ever mentioned by opponents of evolution. They love to grab onto his earlier statement but strenuously avoid admitting that Popper later changed his mind and agreed that evolution was falsifiable. It is too, as Haldane's remark about the hypothetical pre-Cambrian rabbit shows.
Keller equates "fossil evidence that would falsify the theory of evolution has never been found" with "it is impossible, even in theory, to find fossil evidence that would falsify evolution and therefore evolution is unfalsifiable and therefore evolution is unscientific". It's a nice attempt at rhetorical sleight of hand but profoundly stupid when exposed for what it is.
I assume he is, in theory, intelligent enough to know better but prefers to maintain the facade that his belief system is unfalsifiable.