Not really sure if this is what are you looking for but i don't use the config.yml for form themes i set them manually on each file and render everything manually based on what i want the form to look.
An example of how an entry field looks like ( the name in the form class is answer
{% block _suggest_question_manager_answer_entry_widget %}
{% spaceless %}
<div class="multiple-choice-container">
<div class="row form-group">
{{ form_label(form.value, null, {'label_attr': {'class': 'col-sm-2 control-label'} } ) }}
<div class="col-md-12">
<div class="input-group">
<div class="input-group-addon">
<span class="glyphicon glyphicon-record" aria-hidden="true"></span>
</div>
{{ form_widget(form.value, {'attr': {'class': 'form-control'} } ) }}
{{ form_errors(form.value) }}
<div class="input-group-btn">
<button class="add-answer btn btn-default" aria-label="Add Choice">
<span class="glyphicon glyphicon glyphicon-plus" aria-hidden="true"></span>
</button>
<button class="remove-answer btn btn-default" aria-label="Remove Choice">
<span class="glyphicon glyphicon glyphicon-minus" aria-hidden="true"></span>
</button>
</div>
</div>
</div>
</div>
</div>
{% endspaceless %}
{% endblock %}
How i render the prototype
<script id="answer-template" type="text/template">{{ form_widget(form.answer.vars.prototype) }}</script>
And this is how i load my themes ( it's just an example from a wip template didn't move the template file yet )
{% form_theme form _self %}
I choose my form theme manually each time and not using the global config one because at some point prob i had some problems and didn't stay to figure it out .. prob related to crud operations where i was getting double div wraps one from my own html in the prototype and second one from the form theme and that's why i render each field manually