It depends whose VATS patch is being used and which LS2 controller (E40 or E38) and which base factory tune is in there. There are typically 3 and at least 2 of them are different in method. (HPT-EFilive-LS2edit).
VATS overall is a series of steps that prevent starting and each package generally takes a different route. The coils may turn on and injectors may be left off or cycled once with a fire and cut depending on which VATS patch and whether other tests need to be satisfied. Only way to really tell whether something is missing is with a scanner.
