Command blocks can only be obtained by cheating in normal gameplay, they are used to execute server commands automatically. Using them to build a computer in the game kind of defeats the purpose of the exercise, since instead of using the game's physics to build your device, you're now mostly doing scripting with minecraft commands. The author explicitly said they didn't use any in their build.
The confusion might come from the author using commands / external software to generate and assemble parts of the redstone machine. The final machine doesn’t use any command blocks as part of it’s operation, but the description is a bit ambiguous here