### Godot version

4.0 beta 15

### System information

Windows 10

### Issue description

When ticking `apply_root_scale` the scale is not applied to custom collision shape set in importer.
This apply for `shape_type`  Box, Sphere, Cylinder and Capsule

_I tried to fix it myself but i'm a bit confused on how to have acces to the `apply_root_scale` and `root_scale` at the moment where the shape is generated_

### Steps to reproduce

- Add a 3d model.
- Generate physics for the mesh
- Select a `shape_type` for example Box
- Add `root_scale` != 1 and tick `apply_root_scale`

### Minimal reproduction project

[BoxColliderImport.zip](https://github.com/godotengine/godot/files/10500751/BoxColliderImport.zip)

light = memnew(DirectionalLight3D);
	light->set_transform(Transform3D().looking_at(Vector3(-1, -2, -0.6), Vector3(0, 1, 0)));
	base_viewport->add_child(light);
	light->set_shadow(true);
	{
		Ref<StandardMaterial3D> selection_mat;
		selection_mat.instantiate();
		selection_mat->set_shading_mode(StandardMaterial3D::SHADING_MODE_UNSHADED);
		selection_mat->set_albedo(Color(1, 0.8, 1.0));
		Ref<SurfaceTool> st;
		st.instantiate();
		st->begin(Mesh::PRIMITIVE_LINES);
		AABB base_aabb;
		base_aabb.size = Vector3(1, 1, 1);
		for (int i = 0; i < 12; i++) {
			Vector3 a, b;
			base_aabb.get_edge(i, a, b);
			st->add_vertex(a);
			st->add_vertex(a.lerp(b, 0.2));
			st->add_vertex(b);
			st->add_vertex(b.lerp(a, 0.2));
		}
		selection_mesh.instantiate();
		st->commit(selection_mesh);
		selection_mesh->surface_set_material(0, selection_mat);
		node_selected = memnew(MeshInstance3D);
		node_selected->set_mesh(selection_mesh);
		base_viewport->add_child(node_selected);
		node_selected->hide();
	}