### 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)

} break;
					case ANIMATION_IMPORT_TRACKS_IF_PRESENT_FOR_ALL: {
						used_tracks[j].insert(anim->track_get_path(i), 0);
						tracks_to_add = true;
					} break;
					case ANIMATION_IMPORT_TRACKS_NEVER: {
						anim->remove_track(i);
						i--;
					} break;
				}
			}
		}
	}
	if (!tracks_to_add) {
		return;
	}
	uint32_t pass = 0;
	for (const StringName &I : anims) {
		Ref<Animation> anim = p_player->get_animation(I);
		for (int j = 0; j < TRACK_CHANNEL_MAX; j++) {
			if (p_track_actions[j] != ANIMATION_IMPORT_TRACKS_IF_PRESENT_FOR_ALL) {
				continue;
			}
			pass++;
			for (int i = 0; i < anim->get_track_count(); i++) {
				if (anim->track_get_type(i) != track_types[j]) {
					continue;
				}
				NodePath path = anim->track_get_path(i);