### 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)

p_node->replace_by(col);
					memdelete(p_node);
					p_node = col;
					_add_shapes(col, shapes);
				}
			}
		} else if (p_node->has_meta("empty_draw_type")) {
			String empty_draw_type = String(p_node->get_meta("empty_draw_type"));
			StaticBody3D *sb = memnew(StaticBody3D);
			sb->set_name(fixed_name);
			Object::cast_to<Node3D>(sb)->set_transform(Object::cast_to<Node3D>(p_node)->get_transform());
			p_node->replace_by(sb);
			memdelete(p_node);
			p_node = sb;
			CollisionShape3D *colshape = memnew(CollisionShape3D);
			if (empty_draw_type == "CUBE") {
				BoxShape3D *boxShape = memnew(BoxShape3D);
				boxShape->set_size(Vector3(2, 2, 2));
				colshape->set_shape(boxShape);
			} else if (empty_draw_type == "SINGLE_ARROW") {
				SeparationRayShape3D *rayShape = memnew(SeparationRayShape3D);
				rayShape->set_length(1);
				colshape->set_shape(rayShape);
				Object::cast_to<Node3D>(sb)->rotate_x(Math_PI / 2);
			} else if (empty_draw_type == "IMAGE") {
				WorldBoundaryShape3D *world_boundary_shape = memnew(WorldBoundaryShape3D);
				colshape->set_shape(world_boundary_shape);
			} else {
				SphereShape3D *sphereShape = memnew(SphereShape3D);
				sphereShape->set_radius(1);