One idea, off the top of my head, is something like “Onion Skin” or “Photoshop Layers.”
That is, the Pattern Matrix stays intact. Tada! But, you can activate different layers. In these layers you merge squares, lasso notes, name them, and drag and drop them. There’s a post by Psyj that shows something similar for the Pattern Editor. This is also conceptuially similar to PM Clip, in that it keeps track of note structures but isn’t really clips.
These separate “onion skin layers”, on top the pattern matrix, allow me to define chunks of data and move them around giving me the illusion of control, but the reality is just intelligent representation of static data that is auto-merged into regular patterns.