Here's an idea for you, one which I haven't fully thought through but which I will post here in case it proves useful.
For my use case we am required to build the Telerik UI for WPF binaries from the source code. This is because we offer our product as a trial version which requires the source files to be protected.
Building the source takes a bit of time whenever there is a new version and we have to remember to copy and replace the modified source protection files before we build the binaries.
My suggestion would be to move the file protection code into a single separate class library (DLL) and provide the source code that can be modified by the end user and rebuilt into the file protection DLL.
Then rather than having to rebuild the entire source code from scratch whenever there is a new version, we could just use the installer to install the new binaries and just replace the FileProtection.dll file.
That way when there is a new version of UI for WPF (or whatever product) we could quickly update to it and then when we build our product installer we just copy the modified FileProtection.dll to be bundled alongside the Telerik binaries.
As I said I haven't thought this through all the way and there may be excellent reasons why you are unable to do this, but I thought I'd share the idea.
HTH Richard