The problem that you have with Transparent sync in production is that the file system becomes the source of record for your data. This is an issue because it bypasses functionality in Sitecore related to syncing.
From Kam;'s article
Because Transparent Sync bypasses the normal sync process, transparent
sync also bypasses anything that is hooked to sync. This would include
things like custom evaluators (like NewItemsOnlyEvaluator) and the
sync event pipelines. If you are relying on these customizations, turn
transparent sync off for the configurations that use them.
Transparent Sync is great for development because as soon as you pull your update from source control, its automatically synced into your dev environment.
Currently when I use Unicorn in production, I turn off the Unicorn data providers, forcing me to use /Unicorn.aspx and syncing the deployment to Sitecore. I do this with a transformation to my Unicorn.config release file.
<configuration xmlns:patch="http://www.sitecore.net/xmlconfig/" xmlns:xdt="http://schemas.microsoft.com/XML-Document-Transform">