You can use EminentWare's PackageBoot to accomplish this. Be sure to create a duplicate of the EminentWare package first, so any future synch's do not overwrite your changes. Enable PackageBoot and make the necessary edits to the PackageBoot.xml. Instructions are in the PackageBoot.xml, and also in the EminentWare Local Publishing Administration Guide found in the Resources section of our website.
Please contact email@example.com if you have further questions.
supplementally to what Tonya has said,
you can specify command line arguments to use when creating or editing a package.
In the case of a MSI, you can add the TRANSFORMS=mytransform.mst. (check my syntax, memory isnt what is used to be)
Then, the next question is how do we get the actual transform down with the package.
So, in the package editor, you can choose the additional content button (this is the same page where you specify the command lines).
In that dialog, you can add your MST file.
So, when you publish the package, you will actually have 2 files, one MSI and one MST, being published.
You can do this with or without Packageboot, although doing it with packageboot will probably give you more flexibility moving forward.