### 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)

Ref<AnimationLibrary> al = ap->get_animation_library(ap->find_animation_library(anim));
	for (int i = 0; i < p_slices.size(); i += 7) {
		String name = p_slices[i];
		float from = p_slices[i + 1];
		float to = p_slices[i + 2];
		Animation::LoopMode loop_mode = static_cast<Animation::LoopMode>((int)p_slices[i + 3]);
		bool save_to_file = p_slices[i + 4];
		String save_to_path = p_slices[i + 5];
		bool keep_current = p_slices[i + 6];
		if (from >= to) {
			continue;
		}
		Ref<Animation> new_anim = memnew(Animation);
		for (int j = 0; j < anim->get_track_count(); j++) {
			List<float> keys;
			int kc = anim->track_get_key_count(j);
			int dtrack = -1;
			for (int k = 0; k < kc; k++) {
				float kt = anim->track_get_key_time(j, k);