### 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)

bool create_shadow_meshes = bool(p_options["meshes/create_shadow_meshes"]);
	int light_bake_mode = p_options["meshes/light_baking"];
	float texel_size = p_options["meshes/lightmap_texel_size"];
	float lightmap_texel_size = MAX(0.001, texel_size);
	Vector<uint8_t> src_lightmap_cache;
	Vector<Vector<uint8_t>> mesh_lightmap_caches;
	{
		src_lightmap_cache = FileAccess::get_file_as_bytes(p_source_file + ".unwrap_cache", &err);
		if (err != OK) {
			src_lightmap_cache.clear();
		}
	}
	Dictionary mesh_data;
	if (subresources.has("meshes")) {
		mesh_data = subresources["meshes"];
	}
	_generate_meshes(scene, mesh_data, gen_lods, create_shadow_meshes, LightBakeMode(light_bake_mode), lightmap_texel_size, src_lightmap_cache, mesh_lightmap_caches);
	if (mesh_lightmap_caches.size()) {
		Ref<FileAccess> f = FileAccess::open(p_source_file + ".unwrap_cache", FileAccess::WRITE);
		if (f.is_valid()) {
			f->store_32(mesh_lightmap_caches.size());
			for (int i = 0; i < mesh_lightmap_caches.size(); i++) {
				String md5 = String::md5(mesh_lightmap_caches[i].ptr());
				f->store_buffer(mesh_lightmap_caches[i].ptr(), mesh_lightmap_caches[i].size());
			}
		}
	}
	err = OK;
	progress.step(TTR("Running Custom Script..."), 2);
	String post_import_script_path = p_options["import_script/path"];