I think we have a way to do this. First, I'm going to clarify our terminology, since the "bundle" versus "package" naming is important:
Bundle: a bundle is a combination of 2 or more books which can be bought at a discounted price (essentially a coupon for multiple books)
Extra: an extra is something that can be included with a book Package
Package: a package is for a book plus one or more Extras
So, you would do is make a Book, create the Extra, and create two Packages: "The Book" and "The Book Plus Extras".
Now, in terms of how to sell just the extras as an upsell: we don't want books on Leanpub which are empty, and only contain extras. Too many customers would buy the book by mistake (many people don't read descriptions), and refunds cost us money.
A much simpler way to do this is as follows:
Sell the "The Book" for say $10.
In the book, have a note in the preface saying "If you want the extras with this book, use this coupon (coupon link) to get the "The Book Plus Extras" package for only an extra $10. The coupon would discount the "The Book Plus Extras" package to $10.
Readers can then use this coupon to make a second purchase of the book package which includes the extras.
Have this coupon have an unlimited use limit and no expiry date.
Yes, it does mean that a coupon is floating around which can be shared with people, but this is a much smaller risk than no sale.
Also, it does inflate the reader count by 1 reader for every person who does the upsell, but we do not think this is that big of an issue...