You can save an Illustrator graphic as a layered PDF and control the visibility of layers in InDesign. Adjusting layer visibility in InDesign lets you vary an illustration depending on context. Rather than create multiple versions of the same illustration, say for a multilanguage publication, you can place the same illustration where needed and adjust the visibility of the layers as appropriate.
You can transform a PDF as a single object (you can rotate or resize it, for example), but you cannot edit the paths, objects, or text within the illustration.