I don't think that (waiting for the beep as you MF) will achieve any better focus than using AF will - it will beep when the same conditions are met, and the beep will come from the same AF sensor if that's the one you have set.
In theory, you're right. However, in practice, when I slowly
rotate the focus ring (1) it is much more likely to "beep" than with AF, and (2) I trust its accuracy more. I find that, in challenging lighting situations, AF is more likely to "hunt" a few times (because it "tries too hard, too fast") ... whereas with a slow, deliberate MF effort in challenging lighting situations, the camera is much more likely to recognize "the ideal focus" on the first try.
Also, compositionally, sometimes the fixed focus dots don't land on the right spot. So I either have to re-compose the shot, to suit the dots, or I have to focus w/o the dots.
Live View at 5x or 10x will be better than AF in situations where you have time (and support) to use it, because you are seeing the image and not relying on any AF system and its limitations.
I take it you meant MF situations?
But yes, I absolutely agree with you here.