According to the instructions the door lock timer module is removed from it's bracket, disconnected from it's harness and discarded and the keyless entry module is mounted in it's place. The keyless module only has one connection plug so there's no way for it to clip between the two couplers.
I've looked way up under the dash using a flashlight and mirror trying to find another 16 pin connector and can't find any others. The coupler connected to the 16 pin only has four wires, so it certainly isn't using all sixteen pins. I'm beginning to think it was added later for some aftermarket part but I can't imagine what part that would be.