How to assign email template with related module values ?

Doesn't really support this.  I've resorted to sending email in a logic hook or scheduled job, loading the template and replacing the values myself.

How to automatically send email (using a template) when a new Account is created? 

I used this to start with.  I included custom variables in my template (~variablename~), and then replaced them in the body_html and body using php with the actual values. Kinda janky, but you gotta do what you gotta do.