App Engine Adding custom domain verification failed despite main site ownership verified

Finally was able to get it to work by switching the “Instructions for” box to “Any DNS provider” instead of Cloudflare, and then pressing verify. Since the start, I had been putting in the code manually as the cloudflare helper would set it to the root domain no matter what (bug?), but even then verifying wouldn’t work as long as cloudflare was set as the option.

You can get around this by selecting the domain verified property and then removing the root domain and others from the mappings offered and adding your subdomain