First off, you should know that get_post_meta() doesn’t create any custom fields (or metadata), it only retrieves the custom field’s value. But the WordPress functions that do create custom fields (for posts) are add_post_meta() and update_post_meta().
So that get_post_meta($post->ID, "mt_post_subtitle", true) simply retrieves the value of the meta/field named mt_post_subtitle for the post (referenced by that $post) and as I mentioned in the comment, you could try renaming the ACF field from subtitle to mt_post_subtitle and the get_post_meta() call in your single.php (single post) template should continue to work normally.
Alternatively, you could’ve also used the ACF function for retrieving custom field’s value, which is get_field(), but renaming the field name is an easier option in that no code changes needed. 🙂 But for reference, with get_field() and without changing the ACF field name, you’d change that get_post_meta() to get_field( 'subtitle', $post->ID ).