Yeah, I was looking at the same thing. They show you the harness poking out of the hole, but don't show you putting the tee into the bed light harness.
The bed lights can be installed after the truck is built, so you just need access behind the driver's rear tail light. See this guy installing them:
My assumption is you pull the tail light, unplug the bed lights, plug the new harness in between, and also up through your new hole in the bed.
Also, since you tap into the trailer harness for power, assume you are backfeeding the system, so you are taking the interior switch (and it's power distribution module) out of the circuit.