They're sufficient in many cases, but you'll still sometimes need the control of working with COM/etc. directly, and those libraries don't fully save you from platform-specific bugs (e.g: https://github.com/glfw/glfw/issues/2644).
> the app in question has no use for system clipboard in the first place
What do you expect to happen when you copy some text from an external editor into a text field?
A hybrid clipboard system is possible, but adds complexity and won't necessarily eliminate platform-specific bugs.
> No app needs to worry about copying text between text fields, system APIs take care of that
Platform-specific APIs that need to be called using platform-specific implementations, and thus are a reasonable cause of platform-specific bugs.