Reduced test case for locker service dynamic component DOM access.

LSTestButton.cmp

<aura:component implements="forceCommunity:availableForAllPageTypes" access="GLOBAL">

  <!-- public attributes -->
  <aura:attribute name="childCmp" type="Aura.Component" access="PUBLIC"/>

  <!-- component event handlers -->
  <aura:handler name="init" value="{!this}" action="{!c.doInit}"/>

  <!-- markup -->
  <div aura:id="view">
    <lightning:button onclick="{!c.handleMarkupButtonClicked}" label="Use Component from Markup"/>
    <lightning:button onclick="{!c.handleDynamicButtonClicked}" label="Use Dynamic Component"/>

    <c:LSTestChild aura:id="child"/>
  </div>
</aura:component>

LSTestButtonController.js

({
  doInit: function (component, event, helper) {
    $A.createComponent(
      'c:LSTestChild', {
        'aura:id': 'dynamicChild'
      },
      function (newCmp) {
        //Add the new component to the body
        if(component.isValid()) {
          component.set('v.childCmp', newCmp);
        }
      }
    );
  },
  handleMarkupButtonClicked: function (component, event, helper) {

    // Using 'find' to get the item from markup
    component.find('child').stuff();
  },
  handleDynamicButtonClicked: function (component, event, helper) {

    // Using our attribute to get the component
    component.get('v.childCmp').stuff();
  }
})

LSTestChild.cmp

<aura:component access="PUBLIC">

  <!-- public methods -->
  <aura:method name="stuff" action="{!c.doStuff}" access="PUBLIC"/>

  <!-- markup -->
  <div aura:id="findMe"></div>

</aura:component>

LSTestChildController.js

({
  doStuff: function (component, event, helper) {
    var viewCmp = component.find('findMe');

    if(typeof viewCmp.getElement !== 'function') {
      alert('getElement() not available!');
    } else {
      alert('getElement() was found on the view!');
    }
  }
})