Mike,
I may have misunderstood your question, but the issue of forcing a MSI installation to reboot should be independent of how the MSI package is distributed.
I would refer you to the AdminStudio MSI Editor - InstallShield X Professional -and the "System Reboots" help topic. If you really want to force a reboot, then you can add the standard 'ForceReboot' action in your execute sequence and MSI will take care of the problem. Naturally, there are other options to consider.
Allen Saxton
AdminStudio Development