I will try to explain again.
Every template file that is used in the extension that is overriding functionality of core template file will cause this warning.
We think of this as a small precaution to notify the user of this.
You can check part of core code in view.php class that does this check :
if ( $this->has_extensions && $result = $this->extensions->isExtensionResource('T', $filename) ) {
if ( is_file($file) ) {
$warning = new AWarning("Extension <b>".$result['extension']."</b> overrides core template with <b>".$filename."</b>" );
$warning->toDebug();
}
$file = $result['file'];
}