### 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)

AnimationPlayer *ap = Object::cast_to<AnimationPlayer>(p_node);
		bool use_optimizer = node_settings["optimizer/enabled"];
		float anim_optimizer_linerr = node_settings["optimizer/max_velocity_error"];
		float anim_optimizer_angerr = node_settings["optimizer/max_angular_error"];
		int anim_optimizer_preerr = node_settings["optimizer/max_precision_error"];
		if (use_optimizer) {
			_optimize_animations(ap, anim_optimizer_linerr, anim_optimizer_angerr, anim_optimizer_preerr);
		}
		bool use_compression = node_settings["compression/enabled"];
		int anim_compression_page_size = node_settings["compression/page_size"];
		if (use_compression) {
			_compress_animations(ap, anim_compression_page_size);
		}
		List<StringName> anims;
		ap->get_animation_list(&anims);
		for (const StringName &name : anims) {
			Ref<Animation> anim = ap->get_animation(name);
			if (p_animation_data.has(name)) {
				Dictionary anim_settings = p_animation_data[name];
				{
					
					List<ImportOption> iopts;
					get_internal_import_options(INTERNAL_IMPORT_CATEGORY_ANIMATION, &iopts);
					for (const ImportOption &F : iopts) {
						if (!anim_settings.has(F.option.name)) {
							anim_settings[F.option.name] = F.default_value;
						}
					}
				}
				anim->set_loop_mode(static_cast<Animation::LoopMode>((int)anim_settings["settings/loop_mode"]));