### 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)

int bone_idx = skel->find_bone(bone);
						if (bone_idx == -1) {
							continue;
						}
						
						_ALLOW_DISCARD_ skel->get_bone_pose(bone_idx);
						loc = skel->get_bone_pose_position(bone_idx);
						rot = skel->get_bone_pose_rotation(bone_idx);
						scale = skel->get_bone_pose_scale(bone_idx);
					} else if (n3d) {
						loc = n3d->get_position();
						rot = n3d->get_transform().basis.get_rotation_quaternion();
						scale = n3d->get_scale();
					} else {
						continue;
					}
					
					int insert_at_pos = -1;
					for (int k = 0; k < anim->get_track_count(); k++) {
						NodePath tpath = anim->track_get_path(k);
						if (path == tpath) {
							Animation::TrackType ttype = anim->track_get_type(k);
							if (insert_at_pos == -1) {
								
								if (track_types[j] < ttype) {
									insert_at_pos = k;
									break; 
								} else {
									insert_at_pos = k + 1;
								}