Thanks for your post.
The SQL that is created by packager is stored as resources in the C# project, and I don't think you can easily amend these. The generated application does support the /presql and /postsql commands though, so you can supply a .sql script as a commandline option when executing the built package.
If you wanted to incorporate the extra commands directly into your package when compiling, it's perhaps a little trickier and not something i've tried before.
A look at the project shows that the /presql and /postsql switches set a couple of properties in the PackageExecutor class. You'll see the Execute method in there calls:
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RunSQLFile(PreSqlFile, "Running pre-processing script")
The RunSQLFile method is responsible for loading the commands from the file and then passing them to the "ExecuteSQLCommand" method, so i'd look at implementing something around this area to suit your needs - for instance running some commands hard-coded into the app.
Hope that helps.