Mark,
The late Frank Mallory gave this response in a forum when someone raised this exact question:
"Actually, there is a field of study know as "dotology" that is devoted
to analysis, recognition, and cataloging of the paint spots on Mercedes
(no joke).
Most of the paint spots were applied by the special torque wrenches used
by Factory inspectors; when the wrench reached the specified valoe for
that fitting, it squirted out some paint.
Other spots were put on springs, motor mounts, and other components, to
designate their value in shore hardness, etc.
The reason these marks are being studied is that when a car is restored
to 100 point condition, it is considered essential that it have the same
paint spots it left the Factory with.
Frank M."