My question is: If we know that our senses are all mediated through the mechanism of their operation, does that not refute Searle's direct realism?
Short answer? No, it does not.
First, perceptual intentionality is not advocating Cartesian duality, but trying to resolve it. What Searle is doing in this article is arguing against the skeptical Argument from Illusion (AfI) and the related Argument from Science (AfS) that consciousness doesn't immediately apprehend visual experience. AfI/AfS claim consciousness-mediated senses prevent "direct" awareness. Searle argues against this by claiming that "direct" awareness isn't what AfI/AfS claims because there is a difference between constituitive and intentional experience.
1) "all we can ever be aware of is the conscious experience" is a False Dichotomy. We can be aware of the real objects but only in a mediated fashion, "through a glass darkly" as it were.
It's not a false dichotomy; it's a tautology. Experience is vaguely defined by an immediate awareness, and awareness is vaguely defined by experience. In plain language, only that which is aware can experience in the literal sense. Rocks have histories like people, but only aware people have experience. In a narrower sense experience is that which we have first-hand history with. An experienced plumber knows and is aware of plumbing differently than a tyro.
"Either our perception extends all the way to the object-in-itself, or else the only other option is that we perceive only our internal experiences." What about extending to the object but being inherently mediated?
Here's the pith of his argument. There is a dichotomy between language and intentionality as a whole because language is built on something more broadly than truth. Conscious experience (which is subjectively holistic) is composed of many sources of experience. Where as past desire and belief and memories are epistemically indirect because they represent symbolic correspondences to external states of affairs, the aspect of conscious experience called visual experience IS direct even if other forms (that is linguistic or representational) are not. This directness Searle calls presentation. From pg. 14:
"[Visual experience] has a special form of intentionality that I call presentational intentionality Perceptual experiences, visual or otherwise, are in the intentionality sense, directed... Beliefs and desires are typically representations... and states of affairs... But when I see something I do not just have a representation; I have a direction presentation of the object.
Then he goes on to speak about the differences between presentations and representations. The gist of it is that a representation is generally linguistic and symbolic and follows the correspondent theory of truth defined by semantics and linguistic convention, where as a presentation has different conditions of satisfaction.
"The present features of the object I am seeing are [emphasis mine] the conditions of satisfaction - what makes the visual experience 'veridical' - but they are experienced immediately... So there is a causal self-reflecxivity to perceptual experience... Memories and prior intentions... are not direct presentations. You are not immediately aware of the object you remember in way that you are if you actually see it.
Hence, seeing is believing. What Searle is doing is breaking down what he sees as an oversimplification of experience by stating that consciousness supervenes on sensation in a different way than on memories and intentionality generally.
Epistemologically there are five generally recognized sources of knowledge (consciousness/introspection, memory, perception, testimony, and reason); intentionality of perception is different than general intentionality (introspection). In fact, he labels his article Perceptual Intentionality to make clear that his personal theory of intetionality includes gradations among epistemic sources. And this makes sense intuitively, doesn't it? Do you go about considering what is testimonial proof in the same way you do in regards to memory or direct perception? Of course not. So, since there are differences in the sources of knowledge, there too should be differences in the theories.