> The ~foo as backup convention is not part of any standard.

Emacs does foo~ by default, not ~foo.

In either case, you're not really supposed to edit files in sites-enabled. That directory is expected to contain symlinks to files in sites-available. I'm not going to say with any certainty that one of the reasons for this indeed is that the pattern (which was used by apache as well - and perhaps other things before it) protects against accidentally reading backup files, but it's not impossible.

So there's definitely a case of holding it wrong if you end up with backup files in that directory.