But look at post #36. That coin has a "shallow" N and a centered dot between the D and the B, but it was not minted in San Francisco.
Without the orientation of an S to go by it's hard to tell for sure but it appears that numbers 1 and 3 can be ruled out. The left edge of the S would likely show on number 2. Number 4 is possible but maybe the hole wouldn't have reached the bottom of the S. On a genuine SVDB a vertical line drawn along the left edge of the N in Cent should just touch the left edge of the B in VDB. It looks like the line in this cent would fall midway between the D and B.
And, as we have show, there appears to be nothing that is specific to the S-VDB's. All S=VDB's have the characteristics you point out, but they are not limited to just the S-VDB. Again, look at the coin in post #36.