There’s a new button on the Transformations panel, “Edit Contents.” When you’re setting movements and rotations in a Transformation object, you can click this button to go into isolation mode to edit the raw contents of the object. The art here will appear exactly as it did when you created the object, regardless of the orientation you had chosen. You can edit the Art, or add or remove art. When you’re done, just press the Esc key to leave isolation mode and go back to adjusting settings in the panel.
Your orientation will again be as you left it, with the art projected accordingly.
Please be aware that if the bounds of the art changes, the anchor point will move also. The anchor by default is the selection center of the art. A custom anchor point is stored as an offset in relation to the center, so if the center moves it will move also, in which case you will need to re-define your anchor.