We added Custom Domain to a Worker to point to ui.stampy.ai and that works fine, however the top domain (stampy.ai) is randomly serving the Worker instead of the expected original response (a HTTP 301 redirect to stampy.ai/wiki/Main_Page).
I can confirm this is an issue too. Definitely do not use Custom Domains for workers if you have multiple subdomains! The responses get mixed up between different subdomains as soon as you do so, which can have really bad effects on a production site. It is of course my own fault for using a beta product in production ;). Reverted back to a dummy CNAME for the worker
Another thing to note, afterwards you need to flush your DNS cache on e.g. Chrome, because for me the whole change poisoned my DNS cache, leading me to a very generic “403 forbidden — Cloudflare” nginx-esque page for all subdomains associated with the one where I activated custom domains for workers.
I will stress again - do not use this in production. It’s been a pain dealing with the after-effects