### 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)

r_options->push_back(ImportOption(PropertyInfo(Variant::FLOAT, "primitive/radius", PROPERTY_HINT_NONE, "", PROPERTY_USAGE_DEFAULT | PROPERTY_USAGE_UPDATE_ALL_IF_MODIFIED), 1.0));
			r_options->push_back(ImportOption(PropertyInfo(Variant::VECTOR3, "primitive/position", PROPERTY_HINT_NONE, "", PROPERTY_USAGE_DEFAULT | PROPERTY_USAGE_UPDATE_ALL_IF_MODIFIED), Vector3()));
			r_options->push_back(ImportOption(PropertyInfo(Variant::VECTOR3, "primitive/rotation", PROPERTY_HINT_NONE, "", PROPERTY_USAGE_DEFAULT | PROPERTY_USAGE_UPDATE_ALL_IF_MODIFIED), Vector3()));
			r_options->push_back(ImportOption(PropertyInfo(Variant::INT, "generate/occluder", PROPERTY_HINT_ENUM, "Disabled,Mesh + Occluder,Occluder Only", PROPERTY_USAGE_DEFAULT | PROPERTY_USAGE_UPDATE_ALL_IF_MODIFIED), 0));
			r_options->push_back(ImportOption(PropertyInfo(Variant::FLOAT, "occluder/simplification_distance", PROPERTY_HINT_RANGE, "0.0,2.0,0.01", PROPERTY_USAGE_DEFAULT | PROPERTY_USAGE_UPDATE_ALL_IF_MODIFIED), 0.1f));
		} break;
		case INTERNAL_IMPORT_CATEGORY_MESH: {
			r_options->push_back(ImportOption(PropertyInfo(Variant::BOOL, "save_to_file/enabled", PROPERTY_HINT_NONE, "", PROPERTY_USAGE_DEFAULT | PROPERTY_USAGE_UPDATE_ALL_IF_MODIFIED), false));
			r_options->push_back(ImportOption(PropertyInfo(Variant::STRING, "save_to_file/path", PROPERTY_HINT_SAVE_FILE, "*.res,*.tres"), ""));
			r_options->push_back(ImportOption(PropertyInfo(Variant::BOOL, "save_to_file/make_streamable"), ""));
			r_options->push_back(ImportOption(PropertyInfo(Variant::INT, "generate/shadow_meshes", PROPERTY_HINT_ENUM, "Default,Enable,Disable"), 0));
			r_options->push_back(ImportOption(PropertyInfo(Variant::INT, "generate/lightmap_uv", PROPERTY_HINT_ENUM, "Default,Enable,Disable"), 0));
			r_options->push_back(ImportOption(PropertyInfo(Variant::INT, "generate/lods", PROPERTY_HINT_ENUM, "Default,Enable,Disable"), 0));
			r_options->push_back(ImportOption(PropertyInfo(Variant::FLOAT, "lods/normal_split_angle", PROPERTY_HINT_RANGE, "0,180,0.1,degrees"), 25.0f));
			r_options->push_back(ImportOption(PropertyInfo(Variant::FLOAT, "lods/normal_merge_angle", PROPERTY_HINT_RANGE, "0,180,0.1,degrees"), 60.0f));
		} break;
		case INTERNAL_IMPORT_CATEGORY_MATERIAL: {
			r_options->push_back(ImportOption(PropertyInfo(Variant::BOOL, "use_external/enabled", PROPERTY_HINT_NONE, "", PROPERTY_USAGE_DEFAULT | PROPERTY_USAGE_UPDATE_ALL_IF_MODIFIED), false));
			r_options->push_back(ImportOption(PropertyInfo(Variant::STRING, "use_external/path", PROPERTY_HINT_FILE, "*.material,*.res,*.tres"), ""));
		} break;
		case INTERNAL_IMPORT_CATEGORY_ANIMATION: {
			r_options->push_back(ImportOption(PropertyInfo(Variant::INT, "settings/loop_mode", PROPERTY_HINT_ENUM, "None,Linear,Pingpong"), 0));
			r_options->push_back(ImportOption(PropertyInfo(Variant::BOOL, "save_to_file/enabled", PROPERTY_HINT_NONE, "", PROPERTY_USAGE_DEFAULT | PROPERTY_USAGE_UPDATE_ALL_IF_MODIFIED), false));
			r_options->push_back(ImportOption(PropertyInfo(Variant::STRING, "save_to_file/path", PROPERTY_HINT_SAVE_FILE, "*.res,*.tres"), ""));
			r_options->push_back(ImportOption(PropertyInfo(Variant::BOOL, "save_to_file/keep_custom_tracks"), ""));
			r_options->push_back(ImportOption(PropertyInfo(Variant::INT, "slices/amount", PROPERTY_HINT_RANGE, "0,256,1", PROPERTY_USAGE_DEFAULT | PROPERTY_USAGE_UPDATE_ALL_IF_MODIFIED), 0));
			for (int i = 0; i < 256; i++) {
				r_options->push_back(ImportOption(PropertyInfo(Variant::STRING, "slice_" + itos(i + 1) + "/name"), ""));
				r_options->push_back(ImportOption(PropertyInfo(Variant::INT, "slice_" + itos(i + 1) + "/start_frame"), 0));
				r_options->push_back(ImportOption(PropertyInfo(Variant::INT, "slice_" + itos(i + 1) + "/end_frame"), 0));