### 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)

if (anim_node) {
		List<StringName> animations;
		anim_node->get_animation_list(&animations);
		for (const StringName &E : animations) {
			_fill_animation(scene_tree, anim_node->get_animation(E), E, item);
		}
	}
	for (int i = 0; i < p_node->get_child_count(); i++) {
		_fill_scene(p_node->get_child(i), item);
	}
	MeshInstance3D *mesh_node = Object::cast_to<MeshInstance3D>(p_node);
	if (mesh_node && mesh_node->get_mesh().is_valid()) {
		if (!editing_animation) {
			_fill_mesh(scene_tree, mesh_node->get_mesh(), item);
		}
		
		MeshInstance3D *collider_view = memnew(MeshInstance3D);
		collider_view->set_name("collider_view");
		collider_view->set_visible(false);
		mesh_node->add_child(collider_view, true);
		collider_view->set_owner(mesh_node);
		Transform3D accum_xform;
		Node3D *base = mesh_node;
		while (base) {
			accum_xform = base->get_transform() * accum_xform;
			base = Object::cast_to<Node3D>(base->get_parent());
		}
		AABB aabb = accum_xform.xform(mesh_node->get_mesh()->get_aabb());
		if (first_aabb) {
			contents_aabb = aabb;