Why my custom submit handler isn't working in menu item edit form?
Forms can have submit callbacks in two places. Either on the form level or on the button that is pressed. The form level callbacks are only invoked if no button-specific callbacks are specified.

Entity forms generally have the submit callbacks on the submit button, which is usually $form['actions']['submit']['#submit'].

This was the same in Drupal 7, although the node form and possibly others had a backwards compatibility layer that also invoked form-level submit callbacks, but this was removed.