The onError that you get from ApplicativeError has this signature:

def onError[A](fa: F[A])(pf: PartialFunction[E, F[Unit]]): F[A]

While the "native" one in IO doesn't take a PartialFunction:

def onError(f: Throwable => IO[Unit]): IO[A]

That could lead to some surprises if you would rewrite a piece of code from tagless final to IO, or if you are just used to using the onError extension method in other code.