perhaps i'm being way to simplistic but let me give this a shot anyway.
in essence this unexaminable pipeline is any given person's fundamental definitions that such person holds as true in the sense that in mathematics we have axioms of math that require no need of examination. the pipeline is the adhocness "factor" of us all. the point at which we are all reduced to hand waving. our fundamental definitions are so entrenched and are taken as truth hence they bear no need for examination or so we think, but wisdom would hold that one should take into account such definitions even hold that the truth of those definitions must be left open.
analogously with respect to science the pipeline
would be the fundamental definitions that support the superstructure of science, the fundamental definitions that are involved in any given experiment. the scientific method itself, being so fundamental to science could be considered unexaminable in the minds of most scientists.
so the question is then so what? well first of all nature shows us as individuals how intuitively far off from reality we can be. example: Galileon tranformations as opposed to Lorentz tranformations with respect to velocity.
this has also proven to be an example in the history of science of how assumptions we take for granted can be problematic.
so now comes along Dick and says let me try and strip away as many assumptions as i can and then consider reality from a perspective of logic and mathematics and lets see what results. well what results is a picture of reality with out viewing it through the pipeline. we become cognizant of what constraints we are forced into inorder to even consider reality without assumptions afforded us via our senses. so now we can juxtapose the fundamental constraints we were forced into against the fundamental definitions we presumme in our sensual world when we design experiments or think about that world.