Thanks for your post.
You can edit the SQL used in the Schema and Data scripts before the .exe is generated, but you will need to do this through a C# Project.
What you need to do is choose to output the package as a C# project, but make sure that you select to create the project with uncompressed resources. You can set this by unchecking the option 'Compress Generated SQL References' on the last step of the wizard. Once you have created the C# Project with uncompressed resources you will be able to edit the SQL through visual studio.