No.Shouldn't the Z height be recorded in the WCS G54 Table as the distance from in my case Z home as a negative number?
When you set Z Reference at Z home, and then measure tool offsets down from there, then set part zero with one of those tools, the Z value of your G54 offset will be the height of your work surface above or below your tool-measuring surface.
Your "reference tool" -- the length against which all other tools are measured, and which therefore has a height offset value of zero -- in this case is an imaginary tool that just touches your tool-measuring surface when Z is at home.
Your G54 WCS offset for the Z axis is the machine-coordinates position that the reference tool would have to be at, to just touch the work surface.
In this case the machine cannot actually go there, but that does not matter because you will be applying the height offset value for an actual tool -- a significant negative value -- whenever you program Z to go anywhere other than home.