### 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)

ERR_CONTINUE(!used_tracks[j].has(path)); 
				used_tracks[j][path] = pass;
			}
			for (const KeyValue<NodePath, uint32_t> &J : used_tracks[j]) {
				if (J.value == pass) {
					continue;
				}
				NodePath path = J.key;
				Node *n = parent->get_node(path);
				if (j == TRACK_CHANNEL_BLEND_SHAPE) {
					MeshInstance3D *mi = Object::cast_to<MeshInstance3D>(n);
					if (mi && path.get_subname_count() > 0) {
						StringName bs = path.get_subname(0);
						bool valid;
						float value = mi->get(bs, &valid);
						if (valid) {
							int track_idx = anim->add_track(track_types[j]);
							anim->track_set_path(track_idx, path);
							anim->track_set_imported(track_idx, true);
							anim->blend_shape_track_insert_key(track_idx, 0, value);
						}
					}
				} else {
					Skeleton3D *skel = Object::cast_to<Skeleton3D>(n);
					Node3D *n3d = Object::cast_to<Node3D>(n);
					Vector3 loc;
					Quaternion rot;
					Vector3 scale;
					if (skel && path.get_subname_count() > 0) {
						StringName bone = path.get_subname(0);