IA does not create or modify MST files. Instead of creating MST files, the recommended approach is to use the (Un)Install MSI Setup, and if necessary, pass the MST file using the command line parameters.
In addition, MST files can be created using the free Orca table editor.
With IA, there is never any need to call msiexec.exe. Our (Un)Install MSI Setup script command does the exact same thing, but with the added benefit of capturing and displaying native installation progress and errors, all within your own IA setup dialogs. In other words, when you use (Un)Install MSI Setup, the end-user would never even be aware a third party setup is running.
Also, you can safely and invisibly pass your serial number as a command line parameter to the MSI file in the (Un)Install MSI Setup command (passing command line parameters can be done in the Action tab of the (Un)Install MSI Setup dialog).
This illustrates the fact that in 99% of the cases, you do not need to create an MST file with IA.