Yes, the Buynow settings and the html email templates are the only two places to modify the order comfirmation email.
The cart uses one of the 3 following email templates when it sends the email confirmation. The email html templates located off your portal root directory in /desktopmodules/smith.buynow/
* OrderTemplate.htm – standard email template
* SHOrderTemplate.htm – email template used when shipping and handling is combined
* OrderSurchargeTemplate.htm – email template used when surcharge is enabled in the cart
Kevin