I recently had a problem where this email was not being sent out. It turned out that I was not clicking on the approve account button, which is the only trigger for this email to be sent to a new user.
My workflow did not include that button, as I used the pulldown to change the account role to registered.user and then assigned a selection of custom roles depending on the client.
If I set the custom roles and click on the approve account button, it resets the custom roles as well.
So in order to send the email and set the custom roles, I have to save each account twice (the act of pressing the account activate button, performs a role switch and an account save) . There is room for more efficiency here.
Ideally, I would like more information about the system emails, as it was not even possible to know it was sent out. So this issue was discovered much later than it should have been.