This configuration setting serves no purpose. It can be disregarded by using --force easily.
Topic on Manual talk:$wgAllowSchemaUpdates/Flow
To prevent operator error.
On very large wikis,if updates arent applied correctly it can cause downtime. Setting was added to make sure nobody accidentally used it on wikipedia
See discussion at https://static-codereview.wikimedia.org/MediaWiki/92109.html and https://phabricator.wikimedia.org/T31558
Sorry for bringing this back up 5 months later. The concern you're mentioning is an admin running it when it's not the right method for updating. An admin could just type this: "update.php --force", and then this setting becomes irrelevant.