First of all MSI installations are already in a in a distributable format, so there is no benefit to recreating the setup. MSI packages are full of internal references, which cannot be captured and recreated. These internal references are critical to the self-healing functionality of MSI packages and are fundamental to their operation.
Repackaging an MSI may result in uninstall problems and other Windows Installer related problems. Finally, and perhaps most important, when the vendor releases and update or patch (MSP) for the product, it will be designed to update their MSI and not yours. When repackaging, all of the globally unique identifiers (GUIDs) used to identify items in the package are regenerated and will not match up to the updates provided by the software vendor package.
There are no changes that cannot be implemented at install-time using an MST (transform) file. Aside from dictating installation preferences, you can add, delete or change any items you wish. I have had some people challenge the fact that the capabilities of MST negate the need to repackage an MSI. While the statement is certianly a fact- it can admittedly be a very difficult task to carry out when dealing with certian packages. Have you given up on MST and repackaged an MSI? Please rate the applications difficulty and provide comments in the software's Package Knowledge base entry. Fighting with a package right now? The Package Knowledge base may hold some answers for you. Also visit our package development message board.