As an ebook formatter, I include a chapter in the TOC called ABOUT THIS EBOOK which includes version number, etc. It includes a change log. Amazon has a field on its item web page which asks for version number, but if I recall, you enter this field manually -- it doesn't come from the ebook source file itself.
Many item pages on Amazon include something in the book description to indicate if any major changes have been made. That's a good place for the publisher to put this information. The problem though is that some changes are not important to the reader. Often I change the formatting to improve how it looks on different screens. Nobody wants to know about that. Occasionally I fix typos, but generally the publisher doesn't want to publicize these kinds of changes. Sometimes I add/change front matter/back matter for promotional reasons, but the consumer doesn't normally care about that.
The Amazon version number is an integer, so I would not change that version number unless you are making significant changes to the content -- not just correcting typos. However, even when doing minor changes, it's still good to keep a change log on an ABOUT THIS EBOOK page inside the ebook and perhaps on the site of the author or publisher.
If you have two epubs which are different versions of the same file, you might be able to run a program to compare individual files inside the epub (which is just a zip file renamed with the .epub suffix.
I'll mention one other thing. Amazon's method of updating ebooks is error-prone. It frequently messes up updating ebooks; one of my own ebooks won't update on Amazon because I had made some annotations to the earlier edition; that blocks Kindle from updating the file -- in this case, I tried deleting all my annotations, but it still would not update to the later edition.