To test, I downloaded the Phab. VM image from the bitnami website.
Upon starting the VM, I stopped the services:
sudo /opt/bitnami/ctlscript.sh stop
The untouched image loaded into VirtualBox has option values:
phabricator.base-uri : http://10.0.2.15:80/
security.alternate-file-domain : http://10.0.2.15:80/
(Perhaps that IP is mine and was configured on boot, or it comes on the VM image?)
Then, apparently the apps need to be started for bnconfig to work:
sudo /opt/bitnami/ctlscript.sh start
Then I ran the bnconfig tool to change the machine_hostname option to example.com:
apps/phabricator/bnconfig --machine_hostname example.com
Now the option values are:
phabricator.base-uri : http://example.com:80/
security.alternate-file-domain : http://example.com:80/
The image used was provided here:
Conclusion: setting machine_hostname via bnconfig appears to write the same hostname to security.alternate-file-domain.
If you'd like a transcript of my session, I can SSH and copy/paste the commands and output leading to this. Beyond that, I can't spend any more time on this.