### 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)

Vector3 s;
						anim->scale_track_interpolate(j, to, &s);
						new_anim->scale_track_insert_key(dtrack, to - from, s);
					} else if (anim->track_get_type(j) == Animation::TYPE_VALUE) {
						Variant var = anim->value_track_interpolate(j, to);
						new_anim->track_insert_key(dtrack, to - from, var);
					} else if (anim->track_get_type(j) == Animation::TYPE_BLEND_SHAPE) {
						float interp;
						anim->blend_shape_track_interpolate(j, to, &interp);
						new_anim->blend_shape_track_insert_key(dtrack, to - from, interp);
					}
				}
			}
			if (dtrack == -1 && p_bake_all) {
				new_anim->add_track(anim->track_get_type(j));
				dtrack = new_anim->get_track_count() - 1;
				new_anim->track_set_path(dtrack, anim->track_get_path(j));
				if (anim->track_get_type(j) == Animation::TYPE_POSITION_3D) {
					Vector3 p;
					anim->position_track_interpolate(j, from, &p);
					new_anim->position_track_insert_key(dtrack, 0, p);
					anim->position_track_interpolate(j, to, &p);
					new_anim->position_track_insert_key(dtrack, to - from, p);
				} else if (anim->track_get_type(j) == Animation::TYPE_ROTATION_3D) {
					Quaternion r;
					anim->rotation_track_interpolate(j, from, &r);
					new_anim->rotation_track_insert_key(dtrack, 0, r);
					anim->rotation_track_interpolate(j, to, &r);
					new_anim->rotation_track_insert_key(dtrack, to - from, r);
				} else if (anim->track_get_type(j) == Animation::TYPE_SCALE_3D) {