### 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)

singleton = this;
	VBoxContainer *main_vb = memnew(VBoxContainer);
	add_child(main_vb);
	HBoxContainer *menu_hb = memnew(HBoxContainer);
	main_vb->add_child(menu_hb);
	action_menu = memnew(MenuButton);
	action_menu->set_text(TTR("Actions..."));
	
	action_menu->set_flat(false);
	action_menu->add_theme_style_override("normal", get_theme_stylebox("normal", "Button"));
	action_menu->add_theme_style_override("hover", get_theme_stylebox("hover", "Button"));
	action_menu->add_theme_style_override("pressed", get_theme_stylebox("pressed", "Button"));
	action_menu->set_focus_mode(Control::FOCUS_ALL);
	menu_hb->add_child(action_menu);
	action_menu->get_popup()->add_item(TTR("Extract Materials"), ACTION_EXTRACT_MATERIALS);
	action_menu->get_popup()->add_separator();
	action_menu->get_popup()->add_item(TTR("Set Animation Save Paths"), ACTION_CHOOSE_ANIMATION_SAVE_PATHS);
	action_menu->get_popup()->add_item(TTR("Set Mesh Save Paths"), ACTION_CHOOSE_MESH_SAVE_PATHS);
	action_menu->get_popup()->connect("id_pressed", callable_mp(this, &SceneImportSettings::_menu_callback));
	tree_split = memnew(HSplitContainer);
	main_vb->add_child(tree_split);
	tree_split->set_v_size_flags(Control::SIZE_EXPAND_FILL);
	data_mode = memnew(TabContainer);
	tree_split->add_child(data_mode);
	data_mode->set_custom_minimum_size(Size2(300 * EDSCALE, 0));
	data_mode->set_theme_type_variation("TabContainerOdd");
	property_split = memnew(HSplitContainer);
	tree_split->add_child(property_split);
	property_split->set_h_size_flags(Control::SIZE_EXPAND_FILL);