I'm just about to glue the neck onto my GSM-1, and thought I better check this before it's too late.
When I received this kit, the truss rod nut was loose and could move backwards and forwards, to the point where it initially looked like I wouldn't get a cover over it. I pressed it back in, and have checked that I can tighten it and put bow/relief in the neck. All seems to be OK, though it does make a nasty creaking sound while I tighten it.
It's got a double-action truss rod, so can actively create both straighten out and add more relief to the neck. Single action truss-rods can only straighten out a neck (which is normally what's required) but double actin truss rods do allow slightly less accurately made necks to be used where more relief is necessary.
These double-action rods have loose dead-zone in the middle (between straightening and adding curve) which is where the nut was when you first had a look. Some necks creak a bit when the truss rod is used and some remain silent. The truss rod in my GSJ-1 creaked a bit when I adjusted it, but its fine. As long as there's no sign of the neck coming to bits and the truss rod is adjusting the relief, it's doing what it should do. You may find that removing the truss rod nut completely and putting a touch of a light grease on it (like Vaseline) or beeswax, will stop the creaking.