System email customization is not offered at this time.
The only emails that you can customize are Marketing emails.
Marketing > Email Marketing > Settings
Well that's a bit rubbish!! Do customers even get an email of any sort when they order from my site??!! We all pay a lot of money for your service, and something like this, customising email response is surely a basic function to expect.
Yes, they get system emails.
While I do not work for GoDaddy, I do know they watch the forums and are always adding new features to GoCentral. You can keep tabs on those updates here.
Web builders are by their very nature limiting. If you want the flexibility to customize every email and response, maybe consider looking at WordPress with WooCommerce.
With WP and Woo you can customize everything -- including having the ability to designate different order confirmations based on products ordered.
I was just on the phone with GoDaddy this afternoon and was told that this was an option. I was sent a link to help me create my store and this information was not there. Searching I came across this thread. GoDaddy this needs to be implemented. We should be able to simply change the text of the confirmation email. I was forwarded the confirmation email and it says "...Thank you for shopping with us. We have received your order. We'll send a confirmation after your items ship."
I would like to change this as our items do not actually "ship".