### 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)

Ref<ImporterMesh> mesh = mi->get_mesh();
		if (mesh.is_valid()) {
			Vector<Ref<Shape3D>> shapes;
			String fixed_name;
			if (r_collision_map.has(mesh)) {
				shapes = r_collision_map[mesh];
			} else if (_teststr(name, "col")) {
				_pre_gen_shape_list(mesh, shapes, false);
				r_collision_map[mesh] = shapes;
			} else if (_teststr(name, "convcol")) {
				_pre_gen_shape_list(mesh, shapes, true);
				r_collision_map[mesh] = shapes;
			}
			if (_teststr(name, "col")) {
				fixed_name = _fixstr(name, "col");
			} else if (_teststr(name, "convcol")) {
				fixed_name = _fixstr(name, "convcol");
			}
			if (!fixed_name.is_empty()) {
				if (mi->get_parent() && !mi->get_parent()->has_node(fixed_name)) {
					mi->set_name(fixed_name);
				}
			}
			if (shapes.size()) {
				StaticBody3D *col = memnew(StaticBody3D);
				mi->add_child(col, true);
				col->set_owner(mi->get_owner());
				_add_shapes(col, shapes);
			}
		}