Yes, it is true that things that can be broken in DGIV can be found/edited in the scenario file
FailGearFailure 0
FailGearCollapse 0
FailLeftMainEngine 0
FailRightMainEngine 0
FailHoverEngine 0
FailRcs 0
FailSurfaceControl 0
FailComputer 0
FailComputerBlueScreen 0
FailAutopilot 0
FailExtRadiator 0
FailAirbrake 0
FailNoseCone 0
FailCanopy 0
FailAntenna 0
FailLeftTurbo 0
FailRightTurbo 0
FailCargoDoor 0
but the APU is not among them. Then, there is the mysterious third fuel tank of DGIV, which is used to generate APU
exhaust. But setting it to 0.0 does not stop the APU, just (temporarily - until save and reload) disables the visual
effect.
So I guess the best you can do is turn the APU off and try to finish the mission without turning it on.