Hi @cmarq,
The thrust factors in ArduSub are determined based on the thruster forward directions (by which way the front of each thruster is pointing) - the propeller spin direction is considered irrelevant, and is generally handled in software by setting a parameter to reverse the output commands to the ESC if it is relevant to do so. There’s some additional discussion here.
Depending on what you mean, this may be somewhat misguided. The thrust factors are multipliers to form linear combinations of thrust commands for a given target direction, and are normalised for each motion axis.
If you’re planning to factor in small forces like minor pitch contributions from the horizontal thrusters due to not being completely vertically aligned with the vehicle’s center of mass then fair enough, but if you’re planning to e.g. reduce the forward and lateral factors for the horizontal thrusters because they are not fully aligned forwards or sideways then that will just end up limiting the output of those thrusters. There’s a bit more discussion on that here, and possibly in other posts tagged vehicle-design 