### 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)

if (kt >= from && kt < to) {
					
					if (dtrack == -1) {
						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 (kt > (from + 0.01) && k > 0) {
							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);
							} 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);
							} else if (anim->track_get_type(j) == Animation::TYPE_SCALE_3D) {
								Vector3 s;
								anim->scale_track_interpolate(j, from, &s);
								new_anim->scale_track_insert_key(dtrack, 0, s);
							} else if (anim->track_get_type(j) == Animation::TYPE_VALUE) {
								Variant var = anim->value_track_interpolate(j, from);
								new_anim->track_insert_key(dtrack, 0, var);
							} else if (anim->track_get_type(j) == Animation::TYPE_BLEND_SHAPE) {
								float interp;
								anim->blend_shape_track_interpolate(j, from, &interp);
								new_anim->blend_shape_track_insert_key(dtrack, 0, interp);
							}
						}
					}
					if (anim->track_get_type(j) == Animation::TYPE_POSITION_3D) {