I have never used autofocus when digitizing film, so I cannot make a direct comparison. Based on my limited experience -
about 50 rolls of 35mm film - manual focusing works fine, and I do not feel like I would gain anything by switching to autofocus.
My Fuji X-T1 has a Focus Assist button that zooms in the viewfinder, and it can show in-focus areas with highlight peaks in white, red, or blue. When the film grain is in focus, featureless areas of the negative twinkle in the highlight color like stars in the sky. Sometimes I set the camera to monochrome, so the red-colored peaks are more visible against the gray background in the viewfinder. (The RAW file, of course, still captures any color information.)
When I first started copying negatives, I was checking the focus for every frame, but I soon realized that was not necessary. Now, I might check the focus once every 6-8 frames, and when I check, focus adjustments are rarely necessary.
For the past two years, I have been using the Skier Sunray Copybox and negative holder. The Skier negative holder is designed so film strips can be fed through a channel which appears to be about 1mm tall. So the film is not really clamped down, but still, I don't see any signs of bowed film in my results. Before I got the Skier Copybox, I was using the negative holder that came with my Minolta film scanner, and that worked too.
My casual testing indicated I could see a slight softening of fine details due to diffraction starting around f/13, and it was quite noticeable at f/16. So at first I was stoping down to f/11. But later, I discovered f/8 gives me enough depth of field.