### 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)

main_settings.erase("_subresources");
	Dictionary nodes;
	Dictionary materials;
	Dictionary meshes;
	Dictionary animations;
	Dictionary subresources;
	for (KeyValue<String, NodeData> &E : node_map) {
		if (E.value.settings.size()) {
			Dictionary d;
			for (const KeyValue<StringName, Variant> &F : E.value.settings) {
				d[String(F.key)] = F.value;
			}
			nodes[E.key] = d;
		}
	}
	if (nodes.size()) {
		subresources["nodes"] = nodes;
	}
	for (KeyValue<String, MaterialData> &E : material_map) {
		if (E.value.settings.size()) {
			Dictionary d;
			for (const KeyValue<StringName, Variant> &F : E.value.settings) {
				d[String(F.key)] = F.value;
			}
			materials[E.key] = d;
		}
	}
	if (materials.size()) {
		subresources["materials"] = materials;
	}