@Amphagory - I was talking about the firmware software endstops, not the hardware endstops. You can NEVER bypass the hardware endtops (otherwise, what would be the point of them?!)
The reason the firmware software endstops are important is because some firmwares won't allow you to move outside of the virtual software endstop range. For example, if the min software endstops are enabled, it's pretty likely the firmware will prevent your machine from moving to a Z-coordinate that is less than zero. If you were trying to print a 0.1mm layer and your bed was 0.2mm too low, you can see why this would be an issue. You would want to put in -0.2mm for the Z-axis gcode offset in S3D, but the firmware would see the Z-0.1 command and with min software endstops enabled in the firmware, it would clamp the movement to Z0.
So in summary, yes, everything you guys are saying about how to use Z-axis offset in S3D is correct, just keep in mind that if the bed is very badly calibrated, the hardware or firmware endstops may step in. As long as you use the S3D offset for small adjustments, you will be fine.