What does it means to "maintain (or not) Transparency" in Photoshop when placing it in another program like InDesign?
Take the image of the blue circle below as an example. "Maintaining transparency" means when it is placed in a document, the checkered parts around the circle will remain see-through.
If transparency is NOT maintained, the document bounds of the blue circle file will be visible (the white part). The edges around it will no longer be see-through.