Peter,
The Deployment Utility modifies a sequence file in order to update the paths to the different modules.
If you use absolute paths in order to reference your modules the deployment utility will convert this paths to be relative.
If you Change the location directory of one of your modules the deployment utility has to modify the sequence file in order to redirect the steps accessing this module, otherwise it wont be able to find it.
If you want to prevent the deployment utility to modify your sequence files you will have to use relative paths all the time and keep the same directory structure.
It means that you will have to create the desired directory structure in your development system before generating the installer.
Hope it helps.