Well, a peptide bond is really just the chemical bond that ties two amino acids together. A protein consists of long chains of amino acids, called polypetides, that form a 3 dimensional, folded structure, through means of different attractions between the molecules. The folded structure is important for proteins your body produces, like enzymes.
However, when the body digests protein, the folded structure is broken first, and then the peptide bonds as well, for easier uptake into the bloodstream and to make single amino acids available so the body can use them as building blocks. Free form amino acids are, like the name says, "free" of peptide bonds, so that digestion and uptake is much easier and you can deliver the exact amino acids the body needs most to build muscle (not all amino acids are involved in muscle, or structural, proteins).
My best guess to why Yates mentions peptide bond aminos is that the refining process has gotten much better since he wrote that, and also that it is better understood which specific amino acids, and in which ratio, an athlete/bodybuilder needs.
To sum up: free form aminos have much higher bioavailability, meaning faster and more complete uptake, whereas peptide bond amino acids are closer to what you find in "real" food like meat or eggs and may be beneficial before sleeping because of slower uptake, although the last is just a guess on my part.