Alright, I'll go out on a limb here, a longer limb...
I used to have an 03 with the factory tow harness, you know the one with the relays that goes above the rear right wheel well. It did this mystery beep too. before I sold the 03 (long story don't ask) I removed the tow harness knowing I would be putting it in my 04. I had been driving the 04 for about a month already without it. So I installed the tow harness and what do you know, that weird beep I heard every so often in the 03 was transplanted into the 04, so it seems. Hey I know it has nothing to do with the locks, but I thought I would put it out there for an interesting discussion.
On another note, I have another theory. My tailgate locks as soon as I start moving. Then when I reach 15 mph the doors lock. With the tailgate already being locked the motor on the lock can't spin because it is stuck right? Sometimes electric motors make sort of a beep noise if they are stalled out in my experience. I'm one of those that when I was a kid messed around with electric motors, rc cars and stuff like that. I remember specifically hearing a beep or rather a tone come from some motors when you stalled them out. So, really this makes more sense then it coming from the tow harness. It comes from the back too I know because I've heard it more than a few times. Usually I have the radio up, so it has done it more times than I know I'm sure. Anyway, that is my theory and I'm sticking to it... and maybe a little with the harness too, but that seems like a stretch.