WP could address some of this by requiring plugin media/js assets to be copied over to public folders during an 'init' process, while requiring the core PHP code to be outside of the document root/public area. But it would break on certain hosting platforms (I know that years ago, Plesk templates would enforce that nothing could live outside the document root - every upgrade they'd change all PHP permissions to only allow PHP execution inside the document root, perpetuating poor security practices for anyone who wanted to host on plesk-managed servers).