Hi @sietse, welcome to the forum 
Which board are you referring to? There are many possible flight controller boards that are capable of running ArduPilot-based autopilot firmwares.
If you’re trying to use our Navigator board, the latest building instructions are here for now (apologies - we’re still working on getting those integrated into the docs).
The original BlueROV is from well before my time at Blue Robotics, but from my understanding of the frame motion axis factors, reducing the contributions from the two front thrusters for vertical motion should help to avoid outweighing the corresponding contribution from the rear thruster.
The 0.45 value specifically was most likely determined to avoid excessive pitching while trying to move straight up or down. If the center of mass is towards the rear vertical thruster then the front thrusters contribute a little extra to the vehicle’s pitch, which can be balanced out by reducing how hard they push:
Torque (a rotational force / moment) induced by a linear force is determined by its magnitude multiplied by the parallel distance with which it’s applied from the center of mass (CoM) of the body it’s acting upon. Note that neither the parallel distance point nor the CoM need to necessarily be enclosed within the volume of the body itself:
This topic is worth a read for some extra context on understanding the effects of mass (and buoyancy) distribution, and how they can be compensated for, and there are other vehicle-design posts with additional insights
Feel free to follow up if something about that isn’t clear, or you’d like some additional explanation.
By the way, I’ve edited your post to have the code formatted in a code block, so it’s easier for others to read, and to copy for testing. You can read about how to do that (and more) in the How to Use the Blue Robotics Forums post