### 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 (r_occluder_arrays) {
					OccluderInstance3D::bake_single_node(mi, 0.0f, r_occluder_arrays->first, r_occluder_arrays->second);
				}
				mesh->set_name(_fixstr(mesh->get_name(), "occ"));
			}
			if (shapes.size()) {
				StaticBody3D *col = memnew(StaticBody3D);
				p_node->add_child(col, true);
				col->set_owner(p_node->get_owner());
				_add_shapes(col, shapes);
			}
		}
	}
	if (p_node) {
		NodePath new_path = p_root->get_path_to(p_node);
		if (new_path != original_path) {
			print_verbose(vformat("Fix: Renamed %s to %s", original_path, new_path));
			r_node_renames.push_back({ original_path, p_node });
		}
	}
	return p_node;
}
Node *ResourceImporterScene::_pre_fix_animations(Node *p_node, Node *p_root, const Dictionary &p_node_data, const Dictionary &p_animation_data, float p_animation_fps) {
	
	for (int i = 0; i < p_node->get_child_count(); i++) {
		Node *r = _pre_fix_animations(p_node->get_child(i), p_root, p_node_data, p_animation_data, p_animation_fps);
		if (!r) {
			i--; 
		}
	}