You can use the CLI to configure HipChat Server and you don't have to go through the setup wizard at all, however as for automating, I'm not sure if it can be done.
For the command line setup, the top items you need to setup are (Type them in the console to get full list of arguments):
Entering in a license (hipchat license)
Entering a hostname/domain (hipchat network)
Entering in a SSL certification (hipchat ssl)
Configuring the mail server (hipchat email)
And since you are skipping the setup wizard, disable it: (hipchat service --disable-startup-wizard)
It's worth noting that when HipChat Server is first started, it configures network properties based on DHCP, so if you have an static IP's or specific gateways, you can use the HipChat network command to configure that.
As for the owner user, you will need to use this command to set your email:
hipchat service -r firstname.lastname@example.org
Then use the https://<FQDN>/forgot_login to set the password. Afterwards, you should be able to log in.
Hope this helps!
HipChat Server Support Engineer | Atlassian
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