flatten node with non uniform scaling in hierarchy changes its shape

**Describe the bug**
When `flatten` is called, it [uses](https://github.com/donmccurdy/glTF-Transform/blob/98a84642a77c7e48efdc203d786b2985726cacfa/packages/functions/src/clear-node-parent.ts#L34) [`node.setMatrix`](https://github.com/donmccurdy/glTF-Transform/blob/98a84642a77c7e48efdc203d786b2985726cacfa/packages/core/src/properties/node.ts#L121) internally, which [decomposes ](https://github.com/donmccurdy/glTF-Transform/blob/98a84642a77c7e48efdc203d786b2985726cacfa/packages/core/src/utils/math-utils.ts#L77)the matrix with three.js' impl, which does not handle sheared matrix correctly as [documented](https://threejs.org/docs/#api/en/math/Matrix4.decompose).

**To Reproduce**
Steps to reproduce the behavior:
1. Go to and open this example model [untitled.zip](https://github.com/user-attachments/files/21073583/untitled.zip)
2. Click on "Script"
3. Run `await document.transform(flatten());`
4. See the shape change


**Expected behavior**
The shape of mesh does not change.

**Versions:**
- Version: [4.0.2 - git master]
- Environment: [ Browser, Node.js]

**Additional context**

The gltf spec [allowed](https://registry.khronos.org/glTF/specs/2.0/glTF-2.0.html#transformations) nodes to have a `matrix` for transformation, so the matrix could be kept.
Maybe an option can be added to let users decide the behavior to use in case of indecomposable matrices, candidates could be:
* decompose: the behavior now
* skip: skip flatten
* bake: bake transform into vertices (slow)

Start with packages/functions/src/clear-node-parent.ts, packages/core/src/properties/node.ts, and packages/core/src/utils/math-utils.ts, then reproduce the issue with flatten() using the linked example model. Determine how flatten should handle indecomposable matrices—decompose, skip, or bake—and verify that the chosen behavior preserves the mesh shape.

Written by the indexing model from the issue text.