I agree that the pics of these bearings are not that bad. Really not enough that would cause an audible knocking noise.
After college I use to work with a reputable Road Race engine builder that specialized in GM LT5 DOHC V8 engines as well other endurance engines.
I remember the first time he had me "scotch brite" brand new bearings to remove the dry film overlay and what was left was a shiny aluminum bearing which had slight shadowing of the grooves like seen in the pics. They were not glass smooth like the dull grey overlay made them seem, and we would be able to see the actual defects in any bearings before they were ever installed.
We would then take all the freshly cleaned and scotch brited bearings and mix n match bearing halves to get different clearance numbers. That experience opened my eyes on how real blueprinted endurance engines were built with so much attention to detail.
I really bet the OP engine was a victim of something in the wrist pin or cylinder distortion, but was easier for the Ford dealer to get approved a replacement short block based on claiming scored bearings and debris found.
In any case, they got the issue solved, but still leaves a mystery of what the real root of the problem is.
Bingo! Your absolutely correct, those bearings are normal. Engine do have and will always have a dry start to some degree, and thats exactly whats being depicted with the bearings in the pic. I truly wish a Ford trouble shooter would shine in with their rundown test and what their seeing. A cylinder load test tells you so much, and might give areas to look at. But no one has given such test results. I got a buddy of mine to look at the bottom end of my engine with the oil pan removed, and did a bit of investigation. As he says the engine is clean. Cylinders still have the crosshatch marks from the factory and no scuffing can be found on the cylinder walls which would indicate piston to wall issue or rings even. End play is great within specs and the rods feel good. His concern is the wrist pins or a single wrist pin that is . Either to the piston or to the rod having a bit too much clearance. Piston slap but as he indicated it wouldn't be just one single slap, it would be multiple. The sound is singular and not consistent or kind of harmonic in a sense. Not rhythm sort of speak. If it was consistent or rhythmical it would give a better indication of what it maybe. The sound is making is puzzling to conclude.