First off, we think that the Amazon and Apple bookstores are great, and that all finished books should be for sale in both stores. You can sell your Leanpub book yourself in both stores for $0. Or you can pay someone like BookBaby or Lulu to do this for you. We don't try to make any money from you when you sell your book in those stores. We have no lock-in.
Now, we think this makes sense for finished books, but not for in-progress books. While a Leanpub book is in-progress, we feel it makes sense to only be sold on Leanpub, since that way your readers get automatic updates when you publish new versions, etc. If you're writing a book and publishing lots of versions of it while you're writing, the last thing you want to deal with is having to update your book in a bunch of storefronts every time you release a new version.
However, we don't think that this is necessarily true of the other places that sell ebooks. While any Leanpub author is free to sell their Leanpub books wherever they want, we feel that storefronts other than Amazon or Apple don't produce much traffic themselves. (This is true of Leanpub too!) To promote your book, you need to do the work yourself, with blogging, Twitter, etc. To concentrate effort (and PageRank), it makes sense to point people at one storefront in your blog posts, tweets, etc. (We want that place to be Leanpub, obviously -- Amazon and Apple can take care of themselves :) Also, the reason we structured our royalties the way we do is so that you get a better deal with Leanpub, so you'll want to point at Leanpub so you make the most money from your marketing efforts!
One important thing to keep in mind is Leanpub's 90% (minus 50 cents) royalty rate for books at all price ranges. Amazon KDP Select (at the time this entry was written) offers its 70% royalty rate only for books priced under $10.00, and only 35% for books priced $10.00 or more. This is especially relevant if you are writing an academic, technical, or research-heavy book that ought to be priced over $9.99.
Also, Leanpub books are priced using "variable pricing". Variable pricing lets you set both a minimum and a suggested price for the book, and then lets the author choose what to pay. This is a really powerful method for selling ebooks online, as it expands the range of customers, establishes a special connection between author and reader, and even allows some books to be sold that otherwise would not be sold, because the author wants the book to also be available for free (you can set the minimum price to zero, but people can still choose to pay for the book if they want to).