### 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)

decomposition_settings.plane_downsampling = Math::lerp(3, 16, precision);
			decomposition_settings.convexhull_downsampling = Math::lerp(3, 16, precision);
			decomposition_settings.max_convex_hulls = Math::lerp(1, 32, precision);
		}
		return p_mesh->convex_decompose(decomposition_settings);
	} else if (generate_shape_type == SHAPE_TYPE_SIMPLE_CONVEX) {
		Vector<Ref<Shape3D>> shapes;
		shapes.push_back(p_mesh->create_convex_shape(true,  false));
		return shapes;
	} else if (generate_shape_type == SHAPE_TYPE_TRIMESH) {
		Vector<Ref<Shape3D>> shapes;
		shapes.push_back(p_mesh->create_trimesh_shape());
		return shapes;
	} else if (generate_shape_type == SHAPE_TYPE_BOX) {
		Ref<BoxShape3D> box;
		box.instantiate();
		if (p_options.has(SNAME("primitive/size"))) {
			box->set_size(p_options[SNAME("primitive/size")]);
		}
		Vector<Ref<Shape3D>> shapes;
		shapes.push_back(box);
		return shapes;
	} else if (generate_shape_type == SHAPE_TYPE_SPHERE) {
		Ref<SphereShape3D> sphere;
		sphere.instantiate();
		if (p_options.has(SNAME("primitive/radius"))) {
			sphere->set_radius(p_options[SNAME("primitive/radius")]);
		}
		Vector<Ref<Shape3D>> shapes;
		shapes.push_back(sphere);