Transparent Sync is off by default and something you deliberately enable. With Transparent Sync, for items controlled by Unicorn it bypasses the Sitecore database completely. In effect, the filesystem becomes the item data-store.
In regular Unicorn usage, you still use the Sitecore databases, but any items controlled by Unicorn (i.e. specified in a configuration) are additionally serialized to the filesystem.
In environments where you don't want Unicorn to maintain serialized items on disk, you can remove / disable the
Unicorn.DataProvider.config file. This still allows you to use the UI to deserialize items from the filesystem, but it won't update the filesystem as items are edited in that environment.
In a typical scenario, you would have the DataProviders enabled on your development machines so that you can keep the filesystem in-sync with the items as you edit them, and then commit those serialized items to source control. Your other environments, such as production, would have the DataProviders disabled as you would only want to deploy the changes up to them, and not be interested in tracking the changes after that.