Just to be clear, the XYZ parameters in the G10 commands are the offsets of the tip of the nozzle relative to the head reference point. You can choose the head reference point to be wherever you like, but the G10 offsets, G31 offsets for the Z probe and M208 limits must all be specified in terms of the head reference point.
It's probably safest to choose the head reference point Z position to be the lowest nozzle you have (or slightly lower), so that the Z values in G10 commands for other tools are all positive.