Several options are discussed and demonstrated for dealing with setups that require InstallShield's InstallScript in the new "Dealing with InstallScript for Admins video".
It is also possible to include InstallScript as a merge module within a vendor MSI.
You can find the latest InstallShieldScriptingEngine.msm files here:
While there is an ordering issue that would seem to be a problem on the surface whereby the check for InstallScript would occur before the merged installation- it appears that the merge module reorders the sequence to account for the problem.
Find more discussion here: TWO MSI INSTALL