The following filter shows only the top-level custom post type items in page attribute dropdowns (in main edit screen and in quick edit).
Replace the **'my_custom_post_type'** with your custom post type name.

    function my_test($args) {
    	global $post_type_object;
    
    	if ( $post_type_object->name == 'my_custom_post_type') {
    		$args['depth'] = 1;
    	}
    	return $args;
    }
    add_filter('page_attributes_dropdown_pages_args','my_test');
    add_filter('quick_edit_dropdown_pages_args', 'my_test');