I got a look at a copy of the Chicago manual at my college and the guidance in that is a lot clearer than it is on the web site where the whole manual is not available without a subscription.
The reason given for citing a electronic edition of a book is quite clear.
The majority of electronically published books offered for download
from a library or bookseller will have a printed counterpart. Because
of the potential for differences, however, authors must indicate that
they have consulted a format other than print. This indication should
be the last part of a full citation that follows the recommendations
for citing printed books [...].
The manual further goes on to state that;
[...] electronic formats do not always carry stable page numbers (e.g., pagination may depend on text size), a factor that potentially limits their suitability as sources. In lieu of a page number, include an indication of chapter or section or other locator.
Further in the section it deals with unpaginated electronic sources in more detail.
For such unpaginated works, it may be appropriate in a note to include
a chapter or paragraph number (if available), a section heading, or a
descriptive phrase that follows the organizational divisions of the
work. In citations of shorter electronic works presented as a single,
searchable document, such locators may be unnecessary.
It seems form reading the manual that the following are the preferred methods of referencing;
- Page number (where stable ones exist/some new kindle books match the
- Chapter or paragraph number
- Section heading
- descriptive phrase that follows the organizational divisions
If you want to cite in MLA; this blog recommends the following.
MLA 5.7.18 defines digital files as neither on the web or a published
CD-ROM. MLA recommends citing a book on a digital device using the
guidelines for citing a book but replacing the format type (Print)
with the name of the digital file format, followed by the word "file.”
For the “Digital file type” field on the form, enter a file format
such as "EPUB file" (a non-proprietary file format used by Kobo, Nook,
Sony and others). If an e-Book reader uses a proprietary format
(e.g., Kindle), you may use the name of the file type ("AZW file") or,
if this is not visible to you, the name of the device ("Kindle file").
Slawenski, Kenneth. J.D. Salinger: A Life. New York: Random, 2011. N.
pag. EPUB file.
If you are only citing a section or chapter:
To cite a chapter or section written by the author of the book, cite
the book and use an in-text reference to identify the specific section
you're quoting or paraphrasing.
If the introduction or preface is
written by another contributor, fill in the section of the form called
Chapter or Section to cite the author, section title and page numbers.