The GS-911 has a 'routine' that parks them then when you're done it re-engages the steppers to function properly again.
I would assume the BMW factory diagnostic computer does the same. I'm not familiar with any other systems but would assume they function in a similar fashion as well.
So no the EFI computer doesn't automatically re-engage the steppers all on its own, at least during these diagnostic functions.
An illustrious quote from vermin:
"I lie to myself because I am the only one who continues to believe me."