Jou have to insert the distance to your cog not to the center of the centerplates. Have you measure it? I think your
z of the imu coukld be wrong. Check the center of gravity with the lipo´s and then take the distance to the middle of die imu.
the other could be right (control also Z by the gps)
Looks okay to me. I think the previous poster was trying to say your COG is usually just below the bottom plate rather than actually on the bottom plate as the lipos and gimbal lower your COG. But doing it to the centre of the bottom plate will work just fine too! People get really fussy about COG for some reason but you'll not really notice any difference in flight characteristics. As time goes on you may change it as you fine tune things but don't worry about it for a new build.
No. The 2 you have at the moment is about right for starters. 2cm means -2cm just to be confusing. Don't know why DJI did it like this. Cultural differences? So at the moment you're saying the IMU is 2cm below the COG (or center plate). Your actual COG is lower but don't worry about that for now. But if you are worried (as we all are) your COG is probably in line with the bottom of your IMU due to the weight of gimbal and lipos.