Is there any elegant way of excluding form element from 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