The article mentions shallow copy, but does this create a persistent immutable data structure? Does it modify all nodes up the tree to the root?

Yes, if you modify a nested dict/list entry, all nodes above it will be cloned. Here's an example:

  x = [1, [2]];
  var y = x;
  set y.[0] = 3; // clones the outer array, keeps a reference to inner array
  set y.[1].[0] = 4; // clones the inner array here. Outer array is now exclusive so it doesn't need another clone.

  var z = x;
  set z.[1].[0] = 4; // clones both arrays at once