There are good formal cryptography courses, though some of them focus on aspects that aren't relevant to what I'd call "cryptographic engineering". For example, differential cryptanalysis is very interesting, but basically nobody except the IOTA community is silly enough to try and implement their own primitives, so that's not a common problem.

I authored Crypto 101. One of my cofounders co-authored Cryptopals and founded the cryptographic practice at Matasano (as well as co-founding Matasano itself ;)). So for cryptographic engineering, I think the answer is "historically oral, and increasingly written, tradition"?