Determine if menu link is current/active
Have you tried to combine it with item.below? I suppose (not tested) that this could be used to only apply the class to the deepest item within the active trail. The code could look something like this:

{% for item in items %}
  {% if item.in_active_trail and not item.below %}
    set classes = [
       'is-active',
    ]
  {% endif %}
{% endfor %}