Configurable Reply-To email header
Could you please consider adding this to General Settings > Mail and to the email templates?
As far as I can tell the From address of any WHMCS notification is the one that is associated with the SMTP address. This address usually can not be changed because of ISP restrictive policies.
What can be freely chosen is the address in the Reply-To email header. It will determine the To address when somebody replies to a notification. Since different email templates belong to different departments, you would want their replies go to different addresses. Hence the need for Reply-To setting in each email template and a fall back default Reply-To setting in General Setting > Mail.