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In a scenario where client -> server through SSL, the server replies with the set of cert(chain-of-trust) which also contains the certificate pinned inside the client.

Let's say the Root CA is compromised and the setup is this : client -> MiTM -> server

Can't the MiTM just use the set of certs from the server to bypass certificate pinning? Does the pinned cert have to be the leaf-certificate in the chain?

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If the private key of the pinned certificate or one of its descendants is compromised then certificate pinning can't help you.

If the leaf-certificate is pinned, only getting the private key of this certificate allows MitM. If the intermediate certificate one level above is pinned, getting the private key of this intermediate or the leaf allows MitM.

Of course, pinning the leaf also makes it a lot harder to change that certificate.

As always, there is a trade off.

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