The webfinger includes the subdomain. So the webfinger would be either @user@mastodon.domain.com or @user@pixelfed.domain.com, given your example.
Does it still work that way when using the web_domain setting?
I can't speak for those two services in particular, but I know that Matrix will check https://domain.com/.well-known/matrix/server to see what (sub)domain is responsible for domain.com. I suspect other services also use .well-known too.
Yes, they use a webfinger on the .well-known path.
I've thought that if some dev created a webfinger reverse proxy they would be the hero of the fediverse.
I've thought about doing this. It seems simple enough, though it would need a front end to be user friendly. I could build the rest api pretty quickly.
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