Indeed. I took a computer engineering class in undergrad. The capstone project was implementing from scratch a multi-pipeline RISC CPU (including the ALU and a very basic L1 cache) in Verilog that we flashed to FPGAs that we then programmed to play checkers using hand-compiled C. The FPGA was easier to flash and debug than the Spartan-6 mentioned in TFA but was significantly more expensive as well.
It was a brutal class, but it totally demystified computers and the whole industry in a way that made me feel like I really could understand the "whole" stack. Nothing scares me any more, and I no longer fear "magic" in software or hardware.