Irrespective of what the default document root is, whether it is /usr/share/nginx/www or /var/www/html, the issue in this bug report is whether a user should expect to be able to modify the index.html file in the default document root and have those changes respected.
If your answer is that the default document root isn't a place that a user can put files, because certain files will be destroyed by package updates, than I put to you this question: what is the point of having a default document root in the first place?
I submit that everything installed under the default document root should be marked as a configuration file in the package, so that user modifications will be respected. I can't think of any good reason not to do things that way, regardless of what you think the document root should be.
Will Ubuntu fix the package, or does it need to be done by the Debian maintainer?