Live view is pretty accurate at actual pixels, but it is slow. Peaking is nice in theory, but with the stuff I have (Sony) it is not really useful for critical focus.
I would also guess that manual focus has a lot to do with lenses. Lenses built for AF have short focusing throw, may be to short for accurate focus. Also, many lenses have focus shift (focus changes when stopping down) but it is no issue if you shoot fully open with a very good lens.
I guess that practice helps, personally I use either AF or live view at actual pixels on Sony.
On the Hasselblad V I use a prism finder with the acute matte screen that came with the camera and Zeiss Victory 3x monocular that gives additional three times magnification and can be adjusted for eyesight. That works mostly well.
One reason we had less problems with focus on film was that we enlarged less. Going actual pixels on digital images corresponds to extreme size prints. Screen pixel pitch is about 100 PPI, so looking at a 24MP image at actual pixels corresponds to looking a 40x60" print at close distance. How often did we make prints that size and looked close in the film times?
Birdman is right about practice.
Useless for active subjects.