Is there a way for the server to know that requests have been intercepted?
No, because the communication with the server does not use the custom-installed MITM certificate. That certificate is only used by the client when communicating with the proxy.
[Client] <=========================> [Proxy] <=======================> [Server]
Connection using fake Connection using real
user-installed cert/key server cert/key
The server only knows that it is communicating with some client. The server has no idea that that client is actually a proxy acting on behalf of another client. The proxy-to-server connection is a perfectly genuine HTTPS connection, using the server's real key and certificate.
The connection between the client and the proxy is where something fishy is going on. The proxy knows that the certificate isn't genuine, but the proxy is controlled by the person orchestrating the MITM attack, so that's perfectly reasonable.