Christopher's mechanistic view of the world causes him to lack empathy or even sympathy for others, most notably his father. In this passage, however, he shows that the way he views the world actually allows him to understand the ways in which people think and feel with great profundity and without any loss of the logical rigor which characterizes his thought. He says that people imagine their brains are qualitatively different from computers. This is because they think of a pilot "like Captain Jean-Luc Picard in Star Trek" sitting inside their head and looking at a big screen.
This, however, is just a picture that people use to interpret the way they see the world. It is not a special attribute of human beings. Christopher also observes that people think they are unlike computers because computers do not have feelings. However, feelings are also just pictures of what has happened, or failed to happen, or might happen. A computer could easily generate such a picture. Christopher is not only factually correct; his logical mind makes him a brilliant exponent of concepts that have engaged some of the world's most distinguished scientists, such as John von Neumann in his book The Computer and the Brain.
This passage emphasizes that Christopher's "condition," which is not specified in the book (though many readers and critics have assumed it to be Asperger's syndrome) is not a disability but a difference. There are many ways of understanding the world, and the reader who may initially be tempted to focus on what Christopher does not understand is enlightened and perhaps even humbled by the insights in passages such as this.