The transform file path is entered in the Setup.exe MSI Command Line Arguments in Installshield. Everything ok so far.
But when upgrading to a newer version where the server configuration has changed, we'd love the installer to detect changes in the MST file and upgrade the client's configuration when upgrading. The problem now is that the installer uses a cached version of the MST file, and therefore the new configuration wont be applied!
I'll get back when or if I find a solution to this problem.