If it is needed for the compiler to change/update the script file in order to compile I would recommend that it just do change it without warnings. It is okay that you get a warning when compiling manually i.e. from the studio. We have the script files in source control and I would like to know why the script has changes so that I can write that in the commit log.
Also by changing the script file automatically I do not interrupt my coworkers that are using the command-line-only version of the compiler that a script has changed.

Thank for looking into this so quickly! That's one of the reasons that I use SetupBuilder.