I had a similar problem and was able to forward the input events to the viewport in an attached script like this: (The reference to the viewport may need to be adjusted)
func _input(event):
var viewport : Viewport = get_child(0)
viewport.physics_object_picking = true;
viewport.unhandled_input(event)
The script must be added to the viewport.
physics_object_picking must be true.
It doesn't work with _unhandled_input. The forwarding must be done in the _input function.
seeSee also: https://github.com/godotengine/godot/issues/17326this confirmed error report.