The vocaloid girl is actually a very sophisticated and realistic synth, meant to capture and replicate the expression of the notes based on the composer's note velocity (loudness) and whether the note is staccato or legato.
As such, it has been known to produce very accurate 'lalala...lalalaaa' results. However, whatever they're using for the NES tunes (sounds like MIDI files) is not very expressive. Then again, maybe whoever did these isn't using the true vocaloid girl synth, but rather a soundfont of her. Not sure, though.
I should look into this more, haha.