iOS provides an API for integrating 3rd party apps into the Files app. Unfortunately, this API does not offer an option to show the UI to unlock the protection from within the Files app itself. That means, the app protection cannot be easily integrated into the Files app.
If we would allow the Files app integration when app protection is enabled, the Boxcryptor app would be protected, but it could be circumvented by simply opening the Files app and accessing the encrypted files there.
We have some ideas how we can still bring app protection to the Files app despite the missing UI options - however, they are more complex and in order to be ready on iOS 11 release day, we decided to disallow the Files app integration if you want to use app protection. Maybe we will have a better solution in the future.