### 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)

Dictionary subresources = p_options["_subresources"];
	Dictionary node_data;
	if (subresources.has("nodes")) {
		node_data = subresources["nodes"];
	}
	Dictionary material_data;
	if (subresources.has("materials")) {
		material_data = subresources["materials"];
	}
	Dictionary animation_data;
	if (subresources.has("animations")) {
		animation_data = subresources["animations"];
	}
	HashSet<Ref<ImporterMesh>> scanned_meshes;
	HashMap<Ref<ImporterMesh>, Vector<Ref<Shape3D>>> collision_map;
	Pair<PackedVector3Array, PackedInt32Array> occluder_arrays;
	List<Pair<NodePath, Node *>> node_renames;
	_pre_fix_node(scene, scene, collision_map, &occluder_arrays, node_renames);
	for (int i = 0; i < post_importer_plugins.size(); i++) {
		post_importer_plugins.write[i]->pre_process(scene, p_options);
	}
	float fps = 30;
	if (p_options.has(SNAME("animation/fps"))) {
		fps = (float)p_options[SNAME("animation/fps")];
	}
	_pre_fix_animations(scene, scene, node_data, animation_data, fps);
	_post_fix_node(scene, scene, collision_map, occluder_arrays, scanned_meshes, node_data, material_data, animation_data, fps);
	_post_fix_animations(scene, scene, node_data, animation_data, fps);
	String root_type = p_options["nodes/root_type"];
	root_type = root_type.split(" ")[0];