I’m having this same issue. Reading recent posts, it looks like edward is still working on this problem. Arducam_64mp autofocus via picamera2 - #43 by Edward
On that same thread, i found this: Arducam_64mp autofocus via picamera2 - #36 by DaveMcD
which is the code that dave used is: libcamera-still -t 0 -n --autofocus-mode manual --lens-position 2 --width 9152 --height 6944 --denoise cdn_off --gain 9 --shutter 10000 --awbgains 2.0,1.8 --signal -o PiCam1_%04d.jpg --framestart 1
It seemed like it was trying to work for me, but it ultimately didn’t.
So, I still have the same three questions you do.