The WHMCS module just passes in values for all of the fields that would normally need to be set on a per-account basis, and CC uses the template values for the rest. The per-account fields include the hostname field. Yes, if you create an account based on a template via the web interface, and you don't edit the hostname field, then the account will be created with the template hostname... but that's only because you didn't change it.
In a nutshell, this is a feature rather than a bug. Without it, CC would provision broken accounts on servers where different streams are assigned different IP addresses.