If you want to remove the top plate to work on the “middle layer”, the whole drone just falls apart. If you use two thin nuts to hold the arm mounts and bottom plate together, you can then use nuts to hold the top plate on independently. The “Spacer” ensures there is sufficient clamping between the top plate and top of the arm mounts.
The antennae are supposed to be mounted vertically, and not touching carbon fiber. The Antenna Mount uses threaded inserts and bolts between the top and bottom plate on the left and right side of the drone, and you can use double sided tape to hold the antenna.
There is not really a good place to put the Tx, so the VtX mount uses threaded isnerts and bolts onto the bottom plate in the rear to make it nice and symmetrical, and potentially benefits from prop-wash for cooling.