Magento 2: Email Templates Template Style is not Working

First of all, we need to read here: http://devdocs.magento.com/guides/v2.1/frontend-dev-guide/templates/template-email.html#non-inline-styles.

For the Non Inline Styles, they must be in a <style type="text/css"></style> tag for them to work. In your case, we only need to include the header {{template config_path="design/email/header_template"}} in your custom email. Or, we can add the code lines below directly in the custom email:

<style type="text/css">
    {{var template_styles|raw}}
</style>