I think you're a bit harsh on your scope. That's not such a huge difference. Frequency counter is just that - it does one thing and it does it good. Contrary, frequency measurement operates on sampled waveform data points which is powerful in a sense that it can measure all sorts of things, not just frequency, but it's not perfect. It would probably be quite precise if you would feed a very clean sine wave, but if it has noise and harmonics, it just can't get a very accurate result from just a short chunk of captured data. And that is why they include that frequency counter. That's what you are supposed to use if you want any real accuracy.