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I can't remember if it's enabled by default or not, but it's easy enough to enable pprof and get a helpful performance profile from /debug/pprof. See https://caddy.community/t/hangs-on-reload/12010/18 for an example.
I've found that even being unfamiliar with the codebase, it's often pretty easy to identify what part of the call stack is being slow and file a very useful performance but report in GitHub. Check out the profile and see if it leads to any obvious conclusions about why domains are so much slower. There may be some function that's trivial to cache the results of that brings things back to the expected performance.
The profiles were totally different- because the subdomain uses HTTP/3 via the quic-go library. Disabling it globally has it working at 100%