The problem you’re running into is the fact that when ACF creates the options page it sets the function for outputting it’s metaboxes to the field when calling add_menu_page() or add_submenu_page(). In order to customize an options page you need to figure out the hook that is used by WP to run that function and then alter the content that is output by ACF. I have a simple example of modifying the content of top level options page here https://github.com/Hube2/acf-filters-and-functions/blob/master/customized-options-page.php
