This query has been multiple times by our clients and prospects who are planning  to also use Zoho CRM for sending transactional emails to their customer. This currently is also not possible using Zoho Campaigns or Zoho Marketing Hub. 

Zoho is also releasing a product called Zoho Transmail for transactional mails similar to SendGrid or MailChimp. Currently they are in beta version

These email templates  from the CRM are triggered using the "Send Email" option on the various modules for which they are created for. The email templates only allow the dynamic data placeholders from the Modules and the Related Modules  for  Eg a Deal is also related to Contact and an Account. There

It is also very important to note that, for a transactional email to be fired , the data which needs to be sent has to be pushed programatically .

Create the necessary Fields or Columns in the Modules to hold the transactional data and create an email template using those fields.

Currently there is a solution to fire an Zoho CRM email template through deluge  using Zoho Flow  [ Solution Link ]