Customize activation and other system emails
Actually Brad, I was able to figure out a way to do this with some help from @carlcs in the slack channel.

I defined an "HTML Template" in the main email settings screen, then in that template I extend a basic HTML email wrapper, then inside my content block I did this:

{% if emailKey == 'account_activation' %}
    {% include 'mail/activation' %}
{% endif %}
{% if emailKey == 'forgot_password' %}
    {% include 'mail/forgot-password' %}
{% endif %}
{% if emailKey == 'test_email' %}
    {% include 'mail/test-email' %}
{% endif %}
{% if emailKey == 'verify_new_email' %}
    {% include 'mail/verify-new-email' %}
{% endif %}


Then I just created HTML versions of each email within the context of my wrapper.

It works perfectly!