Michael, I don't see why this is unsupported. However, I have a working configuration now. Below I will state the case of what I needed and my situation. I will also state what I did to make it work.
I had two accounts set up 'domain1.com' and 'domain2.com'.
I am setting up a magento store, which allows one to setup multiple stores ( and websites ) given that you can use the same directory of files.
I set up this store initially on domain1 (store.domain1.com). However, I needed to set up a store for domain2 as well. These two stores needed unique I.P. addresses. Here is what I did.
1.) Create Add-On domain in domain1.com.
domain = store.domain2.com
subdomain = anything
path = <path to magento root>
2.) edit DNS zone (I used WHM) to point to the new I.P. Address.
3.) edit the apached config, change to new I.P.:
/var/cpanel/userdata/<domain1 usernmae>/<yourconfig>
(note: I had to edit the document root path as well.. for some reason it did not include 'public_html')
4.) delete cache, main.cache, <yourconfig>.cache
5.) Rebuild apache config (You can do this now, or if you have SSL, do this later.)
/scripts/rebuildhttpdconf
service httpd restart
If you have SSL (which is auto-these days)
6.) click WHM -> SSL/TLS -> Manage SSL Hosts
Look for your domain, if found, I had to delete it and do SSL manually.
7.) After deleting the host, you will want to install an SSL cert manually.
you may need to first go back to your apache user directory and delete any instances of your SSL first.
a.) delete: /var/cpanel/userdata/<domain1 usernmae>/<yourSSLconfig>
b.) delete SSL cache files, if any.
c.) Rebuild apache (see: step 5)
8.) Generate a new CSR (WHM -> SSL/TLS -> Generate an SSL Certificate and Signing Request )
9.) Install the new Certificate (WHM -> SSL/TLS -> Install an SSL Certificate on a domain )
a.) Make sure to assign the right I.P. address in this step.
10.) double check the apache userdate that was created.
/var/cpanel/userdata/<domain1 usernmae>/<yourSSLconfig>
a.) Make sure document root is correct (mine was missing 'public_html')
b.) Make sure the I.P. address is right.
c.) Rebuild apache config (see: step 5)
11.) This should all work now. You can now look at WHM -> SSL/TLS -> Manage Hosts to double check your domain has a record and the right I.P. address.
12.) I turned off autoSSL for the add-on domain because I don't know how it works and didn't want it to overwrite anything.
Disclaimer: Michael noted that this is unsported (which I can't fathom why), so it is probably not recommended you do this. I am doing it out of necessity. Michael, feel free to chime in with any corrections.
