Anyway to programmatically add default fields to a layout?
After hours of perusing, I managed to find a working solution to this issue.  I threw this implementation from InstallService located in craft/app/services.

I realized that CommerceProduct and Variant Field Layouts were set into the Commerce Product Type Model via setFieldLayout() function, therefore all I would need to do is create a new Field Layout with the fields that I required and set them into defaultProductTypes().

    //Write this code in between CommerceProductFieldLayout and Variant type field Layout

    //Any custom fields for your products go here.
    //Format: $yourFieldName = FieldsVariable::getFieldByHandle("Your field's 
handle");
    $bodyField = FieldsVariable::getFieldByHandle('body');
    $tagsField= FieldsVariable::getFieldByHandle('tags');

    //Assemble a new layout that contains the fields you need.
    $infoLayout = craft()-&gt;fields-&gt;assembleLayout(
        array(
            'Content' =&gt; array($bodyField-&gt;id, $tagsField-&gt;id) //Add fields into this array to display your plugins. (e.g. - $YourFieldVariable-&gt;id)
        ),
        array($bodyField-&gt;id) //Add any required fields here.
    );

    // Save Layout into specified product type.
    $productType-&gt;setFieldLayout($infoLayout);