The answer for you is that PHP5.4 added breaking changes compared to 5.3 for shared hosting environments, including:
- safe_mode going away (along with all its friends)
- magic_quotes going away (and as a lot of legacy code relies on it to sanitize, its removal is a bad idea)
- call-time PBref has been removed (this causes a LOT of warnings on legacy code)
- register_globals was thrown off. This completely breaks some legacy code.
So, for that reason, for now, they're keeping PHP5.4 and PHP5.3 both current at the same time. This is the first time this happened in such a fashion, though. You can find the full list of breaking changes here: http://php.net/manual/en/migration54.incompatible.php .