### 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)

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		what = what.substr(0, what.length() - 1);
	}
	String end = p_what.substr(what.length(), p_what.length() - what.length());
	if (what.findn("$" + p_str) != -1) { 
		return what.replace("$" + p_str, "") + end;
	}
	if (what.to_lower().ends_with("-" + p_str)) { 
		return what.substr(0, what.length() - (p_str.length() + 1)) + end;
	}
	if (what.to_lower().ends_with("_" + p_str)) { 
		return what.substr(0, what.length() - (p_str.length() + 1)) + end;
	}
	return what;
}
static void _pre_gen_shape_list(Ref<ImporterMesh> &mesh, Vector<Ref<Shape3D>> &r_shape_list, bool p_convex) {