1) I don't think it is necessarily true that all miracles violate the laws of nature; it may be that he simply "steps in from outside of the Universe" to manipulate things without our knowledge, and then lets nature take its course from that point. To those of us just looking at the events unfolding, it *looks* like a miracle.
An analogy. According to Newton's laws of motion, an object at rest stays at rest, unless acted upon by an outside force. You know, like the screen door which stays shut unless moved by a gust of wind or a cat climbing up it.
But if God or an angel or The Invisible ManTM tiptoed up to the door, pulled it open, and then let it shut, it would look miraculous to us -- because, even though the door was obeying the laws of physics in opening to the pull, and then slamming shut, all we would see is a door opening "by itself".
Creation ex nihilo is different, as presumably the laws are defined at the same time as the cosmos over which they hold sway.
And two other discontinuities would be The Fall and Good Friday / Easter, where the relations of matter and spirit are changed in a discontinuous fashion.
2) God also works through the hearts and minds of Men to effect his will.
A phase shift might entail suddenly collecting information in a planar temporal fashion, thus shifting our 'assimilation' potentials to a completely different frame of reference. ... 'We shall all be changed, in a moment, in the twinkling of an eye.'