Visible crew/equipment: A boom microphone is visible at the top of the screen during Leo Johnson's trial. (00:15:00)
Visible crew/equipment: When James and Maddie meet by the lake, a clear blue trail of cigarette smoke flows in from the right, it's most probably someone's smoke from the crew.
Visible crew/equipment: When Audrey enters her father's office to find him in the middle of his Civil War recreation, a boom mic dips into the shot over their heads. (00:18:40)
Answer: The answer to pretty much any question beginning with "Has David Lynch ever explained _______?" is: no.