WordPress:WPMU Commonly Edited Core Files
Matt said "... I strongly recommend never touching core files".
Although the separation between admin-added and WPMU-distributed files is meant to be total, for various reasons the community does have some files that it finds reason to change.
Many would favour a clean distinction between the core files of WPMU and those that they add or customise. For example, needing to change a core file to change the default blog links is awkward for the administrator trying to keep up to date with the core distribution, and causes noise in the blog. Some
Many of these have tickets in trac so that they can be configuration items.
wp-admin/index.php for default feeds in the dashboard
http://mu.wordpress.org/forums/topic.php?id=1910&replies=5
http://mu.wordpress.org/forums/topic.php?id=1584&replies=6
for allowing only registered users to comment
http://mu.wordpress.org/forums/topic.php?id=1533&replies=7#post-8544
Changing the Hello World Posts
http://mu.wordpress.org/forums/topic.php?id=965&page=3&replies=66#post-10470 http://mu.wordpress.org/forums/topic.php?id=1812&replies=12#post-10607
Short answer: changing this is "beyond the scope of wpmu" as "wpmu follows wp" and there is apparently no need to change it in WP. (Presumbably because in WP the administrator is also the installer, and a generic message fits all.).
Of course, there's also the problem that people try to workaround these posts in other plugins, such as http://mu.wordpress.org/forums/topic.php?id=965&page=2&replies=66#post-10065 - and this creates code bloat.
Preventing comments being interpreted as updates to the blog
http://mu.wordpress.org/forums/topic.php?id=1982&replies=7