### 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)

ImporterMeshInstance3D *src_mesh_node = Object::cast_to<ImporterMeshInstance3D>(p_node);
	if (src_mesh_node) {
		
		MeshInstance3D *mesh_node = memnew(MeshInstance3D);
		mesh_node->set_name(src_mesh_node->get_name());
		mesh_node->set_transform(src_mesh_node->get_transform());
		mesh_node->set_skin(src_mesh_node->get_skin());
		mesh_node->set_skeleton_path(src_mesh_node->get_skeleton_path());
		if (src_mesh_node->get_mesh().is_valid()) {
			Ref<ArrayMesh> mesh;
			if (!src_mesh_node->get_mesh()->has_mesh()) {
				
				bool generate_lods = p_generate_lods;
				float split_angle = 25.0f;
				float merge_angle = 60.0f;
				bool create_shadow_meshes = p_create_shadow_meshes;
				bool bake_lightmaps = p_light_bake_mode == LIGHT_BAKE_STATIC_LIGHTMAPS;
				String save_to_file;
				String mesh_id = src_mesh_node->get_mesh()->get_meta("import_id", src_mesh_node->get_mesh()->get_name());
				if (!mesh_id.is_empty() && p_mesh_data.has(mesh_id)) {
					Dictionary mesh_settings = p_mesh_data[mesh_id];
					{
						
						List<ImportOption> iopts;
						get_internal_import_options(INTERNAL_IMPORT_CATEGORY_MESH, &iopts);
						for (const ImportOption &E : iopts) {
							if (!mesh_settings.has(E.option.name)) {
								mesh_settings[E.option.name] = E.default_value;