I like reading guides like this, and they're useful in a sort of encyclopedic sense, but the problem with them is that they're really a "practical guide to doing every conceivable security thing you could do" with macOS, which is in fact not the best way to secure your operating system. For instance: it's probably not the world's greatest idea to go out of your way to install Adium for secure messaging on a locked-down Mac.

The cryptographic advice in this particular guide is not especially great. You can, for instance, safely ignore what it says about randomness (and, in particular, about how it interacts with FileVault's XTS block crypto). Its advice about password management is needlessly complex (if you trust Keychain, use Keychain Assistant to generate passwords, not OpenSSL --- but most of the cool kids just use 1Password, and they're right to do that).