Super TIU mode has a fewe of quirks (lighting malfunctions, loss of a member engine, inconsistent smoke control), but having the member engines in the active list while building the "lash-up" is definitely what you want to do. In Super TIU mode, I've found that starting the individual engines, then building and starting the "lash-up" works consistently.
From what I've read and in my limited home testing, normal TIU mode doesn't seem to have any of the Super TIU issues (at least I haven't experienced any yet).
