Many of our customers have access to InstallShield, WISE or AdminStudio. These aren't a problem. I'm hoping there is some way I can provide our smaller customers without access to commercial repackaging tools a freely available set of tools and steps to do the file replacement themselves.

Only need to replace a single configuration file inside a compressed MSI, the target user can be assumed to already have Orca installed, know how to use this to customize the Property table (to embed license details for GPO deployment) and have generated an MST file.

Disclaimer: this is very similar to another question but both questions and answers in that thread are not clear.