No one is saying that systems are shutting off anywhere.
I'm just going by what Layne Norton (and Lyle McDonald if I remember correctly) have talked about. Eating protein increases muscle protein synthesis (MPS) and there is apparently a maximum rate of MPS which we get after eating certain amount of protein (depending on the leucine content of the protein source). If we eat more at that time then it's not gonna increase the MPS further at that time because it can't go any faster. You can try googling about this stuff yourselves because I don't really understand it that well.
Don't get me wrong now. I'm a proponent of IF and I don't think this stuff we are talking about is all that critical. Just trying to clarify the article. I don't think theres any question in science whether your MPS will max out after eating certain amount of protein and the effect lasts several hours. I think the question we are interested in is how much this could affect our gains. And going by Cooter and all the guys doing IF, I don't think all that much..
This pic is pretty good advice on the importance of stuff I think: