I could imagine adding an extra line on top of the file - that would be obvious but not too intrusive and allow the same representation in all diff views, including the index editor. Also, it could offer the same intuitive interactions that exist for other differences.

For line endings that will require some more thought, because it may be "normal" to have the checked-in version different from the working tree. Also "normal" depends on the operating system and the git config - offering clear UI support for the CRLF setting, however, would be a tremendous improvement, far beyond the "small detail" of file encodings.

In fact, I stumbled over just this issue. Took me quite a while to sort out what had happened...