Registration is why boards have fiducial marks, but all those marks have been cropped out of the image.
Alignment with a rectangle also doesn't tell us what the connectivity of the pads are, or whether connected pads have solder mask between them. The alignment of parts does not mean there are no solder bridges, but not all solder bridges are defects.
You can check for part presence (easiest). You can check for part alignment (IPC 610 has multiple classes which dictate acceptability of alignment). Neither of these tell us about the solder joint, which is arguably more important, and (in my experience) much more difficult to inspect automatically -- both because it relies on non-visible information which must be considered in the program, but because the solder is simply difficult to image due to its reflectivity.
The clarity and subtle contours of reflection patterns will be susceptible to changes in solder alloy specification or changes in the age of the paste being used. Do better strategies exist? I don't know. I'm just the jerk who had to visually inspect everything when the AOI equipment returned ~100% false positive rates on humid days.
