Scap should touch InitialiseSettings.php after most basic deployments; however, there have been several incidents where a subsequent manual touch of InitialiseSetings.php on tin and a resync of that file have created or fixed new errors.
This happened after the promotion of the train on 2017-05-25 when there were no errors from the promotion of a new version until a subsequent sync of InitialiseSettings.php. And I've seen it happen once recently previously when CommonSettings.php was loudly complaining about a missing variable that was present on all app servers.
I think the expected behavior is to always touch InitialiseSettings.php unless the sync is explicitly a --beta-only-change.