Leanpub books can be generated on Leanpub, and can also be uploaded using our "Bring Your Own Book" feature.
In terms of the layout of Leanpub-generated books: it's pretty minimalist. Over time the custom generation settings have improved, and will continue to do so.
You can export InDesign and do great layouts. Here's why and how.
In terms of uploading a PDF generated from InDesign:
We can also sell books that have been directly uploaded via our "Bring Your Own Book" writing mode.
So, you could do this once your book is done:
Generate the book on Leanpub, and export InDesign.
Do the layout and make a beautiful PDF.
Switch writing mode to Bring Your Own Book on your book's Writing Mode page.
Upload the PDF you made using InDesign, and the EPUB and MOBI that Leanpub generated for you.
However, this would be a huge hassle, since when you wanted to generate another version of your book on Leanpub you'd need to switch writing modes again.
At some point we will probably offer a selective "upload only the PDF" option for use in conjunction with our existing writing modes. But we'd have to make that not confusing to new authors...