Not an expert on eSNI, but my understanding was that the encryption in eSNI is entirely separate from the "main" encryption in TLS, and the eSNI keys have to be the same for every domain served from the same IP address or machine.

Otherwise, the TLS handshake would run into the same chicken/egg problem that you have: To derive the keys, it needs the certificate, but to select the certificate, it needs the domain name.

So you only need to replicate the eSNI key, not the entire cert store.