The message that you receive is a generic message that tells you that when you assign the website (domain or subdomain) to the same directory as the master, this is also acceptable.

As you used the word "Addon Domain", I suppose that you are using a cPanel as administration tool.
When using the cPanel "Addon Domain" or "subdomain" that allows you specifying a "document root", then you have to setup JMS "deploy folder" with the same path and vis versa.

In general, we recommend to start creating the Addon Domain or subdomain in cPanel to let cPanel create the "document root" directory.
After, when you define a JMS slave site and specify a wrong "deploy folder", you receive an error. When both the cPanel "document root" and "deploy folder" give the same path, the deployment is successfull.

What happens in the following situation when working with one domain only, i.e. the main domain.

I've set up the master as a subdomain using the directory structure in the tutorials:
/domains/domain.com/subdomains/master/public_html/

I now want to create a slave site in the main directory so I need to create the following:
/domains/domain.com/public_html/

Because it's a main domain, cPanel won't allow me to handle it as an add-on. How do I then go about mapping www.domain.com to domains/domain.com/public_html/ so that it's the same as the deploy folder?

When the "domain.com" is the primary domain of you cPanel the effectivelly, you can not change the location defined by cPanel.

The solution is to replace the /home/account/public_html directory by a link to your /home/account/domains/domain.com/public_html

You can either do that manually with a SSH terminal command or declare a specific slave site inside JMS where you declare an "alias folder" that point on the /home/account/public_html.
You will rename your /home/account/public_html to /home/account/public_html_old before executing the rule to avoid receive an error on that link.
The "alias folder" present in JMS creates a symbolic link on the "deploy folder".

Thanks