### 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)

List<StringName> anim_names;
	anim->get_animation_list(&anim_names);
	for (const StringName &E : anim_names) {
		Ref<Animation> a = anim->get_animation(E);
		a->optimize(p_max_vel_error, p_max_ang_error, p_prc_error);
	}
}
void ResourceImporterScene::_compress_animations(AnimationPlayer *anim, int p_page_size_kb) {
	List<StringName> anim_names;
	anim->get_animation_list(&anim_names);
	for (const StringName &E : anim_names) {
		Ref<Animation> a = anim->get_animation(E);
		a->compress(p_page_size_kb * 1024);
	}
}
void ResourceImporterScene::get_internal_import_options(InternalImportCategory p_category, List<ImportOption> *r_options) const {