The main reason for that single machine setup is not recommended for Secured eCollaboration, SEP Server and SharePoint, is due to the fact that Secured eCollaboration and SEP Server use the same DLLs in GAC (Global Assembly Cache).
Therefore when updating either SEP-Server or Secured eCollaboration, it is not certain that the DLLs are updated, which could cause functionality issues.
For customers wanting to test Secured eCollaboration this is acceptable, but ONLY on the condition that both Secured eCollaboration and SEP-Server are on the latest versions.
For upgrade procedures on a "one-machine-setup", please follow this step by step process:
1. Uninstall eCollaboration totally with the help of the easy to use: deployment script.
2. Upgrade SEP - Server/MC/Client distribution/client
3. Install new version of eCollaboration with the help of the deployment script.