### 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 == "decomposition/advanced") {
						return true;
					}
					const bool decomposition_advanced =
							p_options.has("decomposition/advanced") &&
							p_options["decomposition/advanced"].operator bool();
					if (p_option == "decomposition/precision") {
						return !decomposition_advanced;
					} else {
						return decomposition_advanced;
					}
				}
				return false;
			}
			if (p_option == "primitive/position" || p_option == "primitive/rotation") {
				const ShapeType physics_shape = (ShapeType)p_options["physics/shape_type"].operator int();
				return generate_physics &&
						physics_shape >= SHAPE_TYPE_BOX;
			}
			if (p_option == "primitive/size") {
				const ShapeType physics_shape = (ShapeType)p_options["physics/shape_type"].operator int();
				return generate_physics &&
						physics_shape == SHAPE_TYPE_BOX;
			}
			if (p_option == "primitive/radius") {
				const ShapeType physics_shape = (ShapeType)p_options["physics/shape_type"].operator int();
				return generate_physics &&
						(physics_shape == SHAPE_TYPE_SPHERE ||
								physics_shape == SHAPE_TYPE_CYLINDER ||
								physics_shape == SHAPE_TYPE_CAPSULE);