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Yes, typically the proxy will listen on 443/80 and all the services it proxies to just use their defaults.
For example: emby.example.tld, port 443 > cloudflare, port 443 > your reverse proxy, port 443 > emby, port 8096
All the client sees is emby.example.tld on port 443 and the resulting web application, everything in between is transparent.