Probably a dumb question, but these seem identical. If a protocol calls for one, can I use the other instead?
Roughly, yes they are similar, but there are processing differences- the real difference is filtering. A product containing simply casein hydrosylate will only be roughly filtered with lots of peptides (like body builder products). Whereas casamino acids should be primarily clean/free amino acids (like nutrients for bacteria).
The actual manufacturing methods will be proprietary for the manufacturer... but you can trust that they are basically doing whatever works best to obtain the individual amino acids and/or whatever is cheapest for obtaining a useable product.
I have used bodybuiling and several other grades of casein products for growing bacteria. I have found that although various products may get the job done there are some serious drawbacks to casein products not intended for growing bacteria.
Differences include clarity of media, cleaning of glassware/fermenter/bioreactor, sudzing of aerated media, and the microorganism. Some microorganisms won't grow very well, and generally, those that can may still not grow quite as well or as fast... so that extra 10% or 20% cfus may be important (or maybe not since the price for quality may be 10 times higher).
The quality-features vs price must be weighed by the grower. Personally, I sometimes autoclave a cheap casein product in one (easy to clean) vessel then rag-filter it into another (then autoclave it again) for growing bacteria... but that's because I have about a thousand pounds of rough casein hydrosylate, and only a kg or so of casamino acids (for particular studies). This method does not eliminate all of the problems but it does reduce some of them.