Can I use the config transforms mechanism of MSDeploy to transform other files?
(another approach)
The msdeploy packaging is jsut invoked during an MSbuild run for your project.
TransformXml is an included task of a .csproj or .vsproj build.
Just modify your build process to invoke that task on whatever file you need.
For example, what we do is write a custom target
Then modify your .csproj to run this BEFORE the Publish task is invoked.