Hi @James Munro,
I'm glad that you were able to resolve your issue and thank you for posting your solution so that others experiencing the same thing can easily reference this!
Since the Microsoft Q&A community has a policy that "The question author cannot accept their own answer. They can only accept answers by others", I'll repost your solution.
Please click "Accept" the answer as original posters help the community find answers faster by identifying the correct answer.
Issue:
Unable to create a custom domain in Azure Front Door because a "custom domain with the same host name already exists"
Resolution:
It turned out that the domain was being used in my subscription, but in a different (legacy) CDN resource. So it seems that a domain can only be used one in the subscription (or perhaps even in a wider scope?).
Once I removed the domain from the legacy CDN, I was able to use it within the Front Door resource.
Please don’t forget to close the thread by clicking "Accept the answer" wherever the information provided helps you, as this can be beneficial to other community members.