When registering a Repository you have the following option in the screen shot below:

I have a cert registered to Port 443 and I select this option everything works.

However, given the Index is still using Port 5053, it seems to me for this to be SSL/TLS communication with the Index Service would we not need to use "netsh http add sslcert" to bind the cert to Port 5053 ( similar to the process for the Notification Service Port 8181)?

There does not seem to be a reference for this in the SSL White Paper.