The graphic editor shows the current height from ground, because that's easier to understand, since the graphic editor it's the only thing you are supposed to use.
But when it saves the settings in the GSX.CFG, they are saved as RELATIVE to the airplane center of mass. This is done to allow a configuration made with a certain payload ( payload = weight = height from ground ), to be used with a different payload. But this is not something you should be concerned with, it's handled by the editor, which will always work.
Your issue is JUST that you are using the wrong GSX.CFG, the one initially uploaded in the sharing section, which had an error in the first door, reading the default variable ( code = 0 ), instead of the custom L: var used by PMDG.
The updated file I've posted in the sharing section is correct.