remove auto generated pages from the menu?

If you don’t want them to ever be listed (using wp_list_pages at least) then you could hide them using a filter

add_filter('wp_list_pages_excludes', 'my_page_excludes');
function my_page_excludes() {
    // the array should contain the page ids you want to exclude
    return array(1,6,7,12);
}

This will stop them from displaying in anything that lists pages using WordPress template functions – including widgets etc. If the user may ever want them to be visible then they’d have to use a custom menu – or you’d have to provide an option to display them.

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