### 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 (p_option == "primitive/height") {
				const ShapeType physics_shape = (ShapeType)p_options["physics/shape_type"].operator int();
				return generate_physics &&
						(physics_shape == SHAPE_TYPE_CYLINDER ||
								physics_shape == SHAPE_TYPE_CAPSULE);
			}
			if (p_option == "occluder/simplification_distance") {
				
				return p_options.has("generate/occluder") && p_options["generate/occluder"].operator signed int() != OCCLUDER_DISABLED;
			}
		} break;
		case INTERNAL_IMPORT_CATEGORY_MESH: {
			if (p_option == "save_to_file/path" || p_option == "save_to_file/make_streamable") {
				return p_options["save_to_file/enabled"];
			}
		} break;
		case INTERNAL_IMPORT_CATEGORY_MATERIAL: {
			if (p_option == "use_external/path") {
				return p_options["use_external/enabled"];
			}
		} break;
		case INTERNAL_IMPORT_CATEGORY_ANIMATION: {
			if (p_option == "save_to_file/path" || p_option == "save_to_file/keep_custom_tracks") {
				return p_options["save_to_file/enabled"];
			}
			if (p_option.begins_with("slice_")) {
				int max_slice = p_options["slices/amount"];
				int slice = p_option.get_slice("_", 1).to_int() - 1;
				if (slice >= max_slice) {