after some more testing I found that to get all the motor control functioning I eventually had to set it up as a motor output. I think this is just due to the way the mixing is done, stabilised throttle output gave me strange readings when I disabled the motor output, it was like it disabled the concept of a motor its strange. I think to get it working with a single motor and not have it assign a set of pins to a second motor that is not used I will need to do a custom mix in the CLI, the sub is packed away at the moment and im working on my other boats I am going to revisit this very soon once some more parts arrive. I was more interested in getting the levelling working that I didn't really do any testing with the motor output. I think most of this is probably due to the stock plane mixing template.
you are right that just passing through the RC input for the throttle might be a better idea since we dont need to worry about any kind of throttle control by the flight controller as most people wont be using any kind of auto navigation.
im going to look into doing a custom mix that will add a dive channel, basically mix an extra input like a slider that will rotate the front and rear planes in the same direction so it can dive as well as use all 4 for levelling.