You may be taking it too literally. The idea is that she and Miss Honey share an emotional bond, tied by their shared history of abuse and desire to help each other, and this manifests in Matilda's storytelling. It's a plot point based more in emotion than logic, like the ending of Sunday in the Park with George.
However, if you need a more literal answer, it is also possible, as you mentioned, that it is part of her psychic powers, just like her telekinesis.
Updated On: 4/22/16 at 04:18 PM