If I have counted correctly, there are at least three involved in aircraft creation and debugging:
Firstly, the 3D model. The SDK says “In the Z axis the center should be approximately where the water level would be”. Meaning that positive Z is upwards. Which matches what most people would call the Z axis, I guess. And positive X is to the left, positive Y is towards the back of the aircraft. A right-hand coordinate system. OK.
Then, when talking about the aircraft once inside the sim, the SDK says “longitudinal (z), where to the front is positive and to the back negative, lateral (x), where to the right is positive and to the left negative, vertical (y), where vertically up is positive and to the down is negative” OK. This now suddenly then a left-hand coordinate system, and all axes different from those in the 3D model. Fun (not). But I guess some deep legacy reasons. And I guess the idea is that different people work on the 3D model and the flight model anyway. (Haha, maybe at companies like Asobo or Aerosoft, but not the case for individual add-on developers.)
But that is not all. If you look in the “Debug Aircraft Weight” window from the Aircraft Editor, there suddenly is this text, applying to part of the values: “Negative is forwards! Offset backwards from Datum”. Ouch.