Thanks for getting in touch! I am going to have to make some assumptions here, so please correct me if I am wrong.
If you have your config file as part of the package, I would suggest using the Substitute Variables in Files feature as is, then using a PowerShell script to move the file to the location after this has occurred.
If the file already exists in that other location, would it not already have the correct variables, or is it part of another deployment package?