I've got a 12-pin plug on my car and van and there ARE unused pins in the 5-pin side.
The trouble with wiring it up differently to "normal" is that trying to use someone else's trailer means either a custom adapter or a rewiring job. I hate borrowing some trailers because the owners custom-wire their plugs then expect my to tow their car somewhere with it so they can get the car fixed. You know how it goes. Pin 4 exchanged with pin 5 so whenever you indicate to the right, the trailer brakes come on, and when you press the brake, the right indicator comes on ...
If you want to do it differently, make is so that you cover YOUR trailer in a standard way and supply the power through a connection in a more effective way as well. It's as easy as sharing the path - two wires connected from point A to point B will share the power passing from one point to the other.
Easy to do. Leave the 12-pin plug in its standard setup. Cut the wire for pin 5 about 100mm back from the plug on both sides. Also cut pin 3 on both sides (which is your earth). Grab some (about 300-400mm) heavy gauge cable (say that 6mm stuff if you're happy with it) and cut it in half. Now in that middle cut, install an Anderson plug.
On one end of the cable, introduce the black lead to the pin 3 cut on the trailer (so there will be 3 wires going into the joiner). Do the same with the red cable of your heavy gauge wire on pin 5. Repeat this for the other end of the cable on the car.
I've just drawn a simple diagram showing what I'm trying to talk about. Hope that makes it clearer! If you do this, most of the power won't pass through the trailer plug, it will follow the heavy cable (path of least resistance).