Just an update for this for anyone following, I found a partial solution that fixes posting custom taxonomies with meta_box parameter via rest api.
In file mb-rest-api/class-mb-rest-api.php line 155 is
$field = rwmb_get_registry( 'field' )->get( $field_id, $object->taxonomy);
It should in fact be:
$field = rwmb_get_registry( 'field' )->get( $field_id, $object->taxonomy, 'term' );
I will continue investigating why builtin taxonomies do not get their meta_box fields passed in and saved at all.