Not a book, but MIT OCW has a class on Aircraft Systems Engineering 16.885J (focusing on the Space Shuttle) that is an excellent example of this. The class starts by looking at the requirements for the system, then examines every single subsystem on the Shuttle, and explains, in detail, why it was built the way it was. Almost always the answer is "because of the constraints placed on the system by the rest of the vehicle" + it has to be as light as possible.

I initially watched the lectures because of an interest in aerospace and it is a fascinating historical series in its own right with some incredible speakers. The lessons for systems engineers are numerous too.