Is there any elegant way of excluding form element from the `values` array of the `FormState`? I know that the values array can be cleaned up in the validation or submit callback, but can we somehow mark the element itself to be not put in the values array of the FormState?
Not within the building of the form as far as I know. You'd need to strip out the values you don't want in the submit handler as you mentioned.

This is probably the easiest way to remove the default form values:

$values = $form_state-&gt;cleanValues()-&gt;getValues();


That will remove: form_id, form_token, form_build_id, op