The generally accepted rationale behind the post-exercise chocolate milk/protein-based recovery shake thing is that there’s a short, 30-minute, glycogen window after hard exercise where your body replenishes the glycogen stored in muscles and liver more rapidly – miss it and it takes longer to replace the depleted stores.
The reason for the protein element is that some research apparently shows that carbohydrate mixed with some protein – chocolate milk etc is about the optimum ratio – is absorbed more rapidly than carbohydrate alone. Viz, it’s there to speed up the absorption of the carbohydrate.
Given that muscle/glycogen supplies get hammered by anaerobic stuff, it seems logical that it’s more important after intense sessions than less brutal ones. That’s the supposed science anyway. And it seems to work for me in real life, though I’m hardly an elite athlete.
The protein during exercise thing I’m less aware of. Like I said above, I’d try it out in training and see how your body reacts.