The smaller pattern means one stop less light for the meter.
Not a problem until you hit the very low end of the meter's sensitivity
range. I have seen the meter drop out in really dark surroundings
(it's an early version). The M6 meter will drop out at some low
light point, and doing this spot reduction just takes you one
stop closer to that point.
Don't use a felt-tip marker (like a "Sharpie") to
do this. If you use a wide angle lens (the Super Angulon), you
will get some oblique reflection from the corners in the highest
contrast situations, and this could throw you off. Sharpie ink
is black but it's also glossy at oblique angles.
Just reduce the size of the dot by filling-in the edges until
it's half the original size. You'll know, when the light meter
reads exactly one stop down. So when using the camera just set
the film speed dial one stop faster.
(Yes, you can modify your Super Angulon
to meter on the M6.)