I have 4 Domains, 1 Forest Root, 3 children. The children are nearly replicas, and have their machines named the same in all 3 child domains.
For Example:
DC1.dev.example.com
DC2.dev.example.com
DC1.test.example.com
DC2.test.example.com
DC1.prod.example.com
DC2.prod.example.com
From what I can tell, the only issue is the SPN duplication on domain join that requires manually fixing.
DC1.dev.example.com
HOST/DC1
HOST/DC1.dev.example.com
The shortname is a duplicate, so when I add test, the SPNSET function of the AD Domain join process fails, if I manually enter the fqdn in the computer name (extended attributes, service principle names) all is well.
Can I prevent the shortname from being added to SPN?
"Can I prevent the shortname from being added to SPN?"
No.
But you can automate it with a script to add the machines to the domain, including following up with the manual changes. That way you can automated the whole process.
These links should help with that.
http://powershellblogger.com/2015/10/join-computer-to-domain-with-desired-computer-name-and-ou/
https://technet.microsoft.com/en-gb/library/ee617263.aspx