### 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)

scene_import_settings_data->settings = &nd.settings;
			if (mi) {
				scene_import_settings_data->category = ResourceImporterScene::INTERNAL_IMPORT_CATEGORY_MESH_3D_NODE;
				scene_import_settings_data->hide_options = editing_animation;
			} else if (Object::cast_to<AnimationPlayer>(nd.node)) {
				scene_import_settings_data->category = ResourceImporterScene::INTERNAL_IMPORT_CATEGORY_ANIMATION_NODE;
			} else if (Object::cast_to<Skeleton3D>(nd.node)) {
				scene_import_settings_data->category = ResourceImporterScene::INTERNAL_IMPORT_CATEGORY_SKELETON_3D_NODE;
			} else {
				scene_import_settings_data->category = ResourceImporterScene::INTERNAL_IMPORT_CATEGORY_NODE;
				scene_import_settings_data->hide_options = editing_animation;
			}
		}
	} else if (p_type == "Animation") {
		node_selected->hide(); 
		mesh_preview->hide();
		if (Object::cast_to<Node3D>(scene)) {
			Object::cast_to<Node3D>(scene)->show();
		}
		
		material_tree->deselect_all();
		mesh_tree->deselect_all();
		AnimationData &ad = animation_map[p_id];
		scene_import_settings_data->settings = &ad.settings;
		scene_import_settings_data->category = ResourceImporterScene::INTERNAL_IMPORT_CATEGORY_ANIMATION;
	} else if (p_type == "Mesh") {
		node_selected->hide();
		if (Object::cast_to<Node3D>(scene)) {
			Object::cast_to<Node3D>(scene)->hide();
		}