Just use a screw driver to close the "catch" for the open hatch.
I do this to capture a rope loop in the catch when I have things in the back that are to long to fit, so I can tie the lift gate down. The other end of the rope I tie to the hitch. To undo the rope I just pull on the lift gate "open" handle.
Anyway, closing the "catch" all the way (2 clicks), will turn off the interior lights as well as get rid of the hatch open warning...
This will work on the flipper glass as well as the lift gate.
Only thing you have to remember is to pull the "Open" handle, before you attempt to close the hatch.