We recently had an MSI go out the door with a bad bug in a custom action. I was able to create a transform for the MSI binary table and this did work but I think I was lucky. I altered the custom action (Installscript), compiled the script and then exported the binary table. I imported the binary table into a copy of the base MSI and then created an MST from the base MSI and the copy with the new binary table. I basically replaced ISSetup.dll by doing this.
My question is, was I lucky to get this to work? What are the pitfalls of this process that I'm not thinking of and is there a better way to do this?