I don't think that makes much of a difference - having it as a managed element or not. I think it has more to do with peering off a Presence Server and a CM and a AES for configuring "how to get Presence Server A the status of Cal's TDM phone on CM A with AES A"
As far as I've seen, the certificate signing request stuff for AES is all manual or via SCEP and that configuration in AES is independent of how System Manager is set up for managed elements. To say, I've done the AES cert stuff before without it explicitly being a managed element and having it be a managed element didn't change the procedure one way or the other.