To avoid the scenario, the image can be captured as .wim, as this imaging format does not exhibit the issue.
If the image has already been captured, then a Windows post-installation task can be used to delete the existing files and also to create new symbolic links.
To create a symbolic link as a post-installation task, use a batch Windows task with the command line 'mklink'
mklink %systemdrive%\path\to\symlink.txt %systemdrive%\path\to\original\file.txt
*note the extension used on the symbolic link matches the extension on the original file.
*Note that hardlinks and symbolic links to directories do not have an issue.