hook_form_FORM_ID_alter() does not take into account weight

When using hook_form_FORM_ID_alter() it will run before the implementation of hook_form_alert() in other modules. Furthermore changing the weight is ignored.
This means hook_form_node_type_form_alter() cannot be used to eg add a form to the "comment settings" of a story, whereas the same will work for the identity.

Will work:

function hook_form_node_type_form_alter(&$form, &$form_state) {
$form['identity']['some_comment_block'] = array();
}

Will not work:

function hook_form_node_type_form_alter(&$form, &$form_state) {
$form['comment']['some_comment_block'] = array();
}