Adam,
Interesting observations!
I wonder if it has something to do with perception, i.e. CBM-Raynor never pretended to try to be natural, so you discount that. Von Hagge (and most others later) used mounds to block views, frame views, and define fairways, but they probably thought that by using free form mounds they were emulating nature.
So, we don't care about Mac's obvious artificiality because he doesn't. But if the gca tries to pretend he is emulating nature to some degree, well then, its open season on critiques?
BTW, I consider your example of a Mac green elevated, by virtue of digging the bunkers down, which may have been intentional to preserve the background. But you will notice how having the green elevated that the sun hits it and makes it clearly visible, which was probably intentional as well. In golf architecture, you generally do what you can to highlight the main features and targets, and sometimes use mounds or trees to hide other less desirable elements around the course. Each has its place, and as you say, it really is a matter of excecution.