You can already do that because email template supports the same variables as themes. For example, if you want to have different template for overdue invoices than for other invoices, here is the pseudo-code:
{% if emphasis.text == "Overdue" %}
Dear Client,
Your invoice is overdue.
{% else %}
Dear Client,
Please see your invoice
{% endif %}
Then see what happens when you try to email overdue invoice and what happens when you try to send invoice that is not overdue.