If you edit MSI with PACE Suite, you can manage files, directories, permissions, registry entries & registry permissions, shortcuts, features/components structure, custom actions and other resources of your package. Also, you can create patches, package documentation, validate your package and publish it to SCCM.
Please note that if you’re editing a vendor MSI (produced by a software manufacturer), according to Windows Installer best practices, you should do it with a transform file. In case you’re editing your repackaged MSI or you are not afraid of losing vendor’s support, skip the step of creating a transform file.