Always use a custom-template. You can create custom templates even for files that don't currently use templates. eg:
/etc/e-smith/templates-custom/etc/udev/permissions.d/51-udev.local.permissions
Also (if needed) make sure and create a templates.metadata file to set the user and perms of the expanded file.
Major upgrades require that you move your custom templates and apply them one at a time after you upgrade. This way you know which ones work and which ones need to me modified. If COS5 changes this, then you will need to update your custom template after the upgrade.
Also, if you make a custom template, you will always be able to find your changes in the templates-custom tree.