Native UI toolkits (with “native” defined as system standard) have system hooks and access to functionality that third party toolkits don’t. Not sure about Android but on iOS I’m pretty sure that a Flutter app would have a battery impact closer to that of a 2D game than a traditional app, even if it’s reasonably efficient.
I believe the current situation is that first-party toolkits have much more insight into the OS and underlying platform than third-party developers can afford.