### 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)

AABB camera_aabb;
	float rot_x = cam_rot_x;
	float rot_y = cam_rot_y;
	float zoom = cam_zoom;
	if (selected_type == "Node" || selected_type.is_empty()) {
		camera_aabb = contents_aabb;
	} else {
		if (mesh_preview->get_mesh().is_valid()) {
			camera_aabb = mesh_preview->get_transform().xform(mesh_preview->get_mesh()->get_aabb());
		} else {
			camera_aabb = AABB(Vector3(-1, -1, -1), Vector3(2, 2, 2));
		}
		if (selected_type == "Mesh" && mesh_map.has(selected_id)) {
			const MeshData &md = mesh_map[selected_id];
			rot_x = md.cam_rot_x;
			rot_y = md.cam_rot_y;
			zoom = md.cam_zoom;
		} else if (selected_type == "Material" && material_map.has(selected_id)) {
			const MaterialData &md = material_map[selected_id];
			rot_x = md.cam_rot_x;
			rot_y = md.cam_rot_y;
			zoom = md.cam_zoom;
		}
	}