If these clusters are just using automated operations like git clone from SSH or HTTP, I don’t think you will run into any issues using two domain names. But if you are doing operations from the web interface like opening issues, tracking time, etc. some of these will be broken if ROOT_URL does not match the domain name.
If possible with your setup, I would recommend setting ROOT_URL to the domain that will be used for the web interface and making sure users only access that domain name for the web interface. Automated operations should still work on domain names that aren’t ROOT_URL.
A follow-up to this post:
Thanks to @wxiaoguang’s and others’ hard work, multiple domain names should no longer cause issues with the UI when 1.19 is released. The warning has been removed from all pages in 1.19 and only shown on the admin page (see #22836).
It will still cause some disparity with regards to email notifications, HTTP clone URLs, webhooks, and others. Those will still be generated with ROOT_URL so it is still best to set it to the main URL that users are expecting.