Each module goes through the system from top to bottom. That means that for any given module, material in the config file will always be read and executed before material in .htaccess. Within any given config or htaccess file, RewriteRules are executed in linear order. Not even your host can change this.
Did you fine-tooth-comb your control-panel settings? Mine (not CP by name) doesn't have anything about index files but it does have a with/without www option.
(Aside: Yes, this can theoretically lead to a double redirect. But only if a user requests a renamed page with the wrong form of the domain name, which is not easy to do by accident, since bookmarks and browser history will record the correct name. They'd have to be typing from memory in one of those ### browsers that sticks www. onto the front of anything you type, on a site whose preferred form doesn't use www. In practice I just get the occasional 301-to-403 sequence, which is no skin off my nose.)
When you say "without index.php" you mean something like
getting 301-redirected (not silently rewritten) to
getting 301-redirected to
which in turn gets rewritten (not redirected) to
The second version is a completely different and unrelated situation so I want to be sure.