1. The background of InDesign's PDFs are transparent. Just open one in Photoshop, for example, and you'll see.
… The fact that your PDF viewer draws a white rectangle at the bottom has nothing to do with InDesign. What would you expect when viewing a “transparent” PDF on your computer — your desktop background? the electronics of your monitor? (And if you print that same PDF on your desktop printer, should the paper come out transparent?)
2. Rounded corners are not supported in the PDF specification.
You cannot compare PDF with SWF in almost any way.
PDFs are 'electronic pages'. The PDF format is not designed, nor meant, for about anything else than displaying a page on a computer.
SWF is best described as 'an animated image program'. An SWF cannot 'exist' on its own, it has to 'run' inside something else, such as a web page. Even when it's a single static image, it still has to “run”, because it's really a little program at heart.
Best advice is not to try to use software and documents for things they are not designed for. You would not think of making an entire book using 72 dpi bitmaps drawn with Paint, would you? For your intended purpose, the PDF file format is not suitable; and using InDesign to create an e-book with, is using the wrong software.