.MST Upload in Managed Installation Detail Screen
Its hard to believe that this isn't already in the system. I am aware I can set up a Scripted install to complete this, but wouldn't be better to just upload a .mst file and have the Managed Install handle the formatting of the install command?
It could have a "Browse..." button to upload an .mst file when a .msi file is detected in the associated file section. Yes, two files will be associated to the install, but they can have the same name (ex: installme.msi and installme.mst). When the .msi file is deleted the other would be as well. Then you can just put a trashcan next to the .mst file to delete it if the user wants.

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Jon commented
Or, you can have a "Manage Transforms" tab somewhere that allows you to use the same transform on multiple installations. Those transforms could either be located in the local shared folder on the server, or in a network location that is accessed using a specified credential.