So yeah I think machines that need to be rotated (batboxes, transformers, etc.) should have a GUI button that you can click to change its direction, because using the wrench doesn't work very well when you are trying to rotate it to face down and there is a block beneath it.
EDIT: Another idea would be to make is so that when you shift-right-click the batbox (etc.) with a wrench it makes it face away from the player instead of toward the player.