### 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 (p_options.has("import/skip_import") && p_option != "import/skip_import" && bool(p_options["import/skip_import"])) {
		return false; 
	}
	switch (p_category) {
		case INTERNAL_IMPORT_CATEGORY_NODE: {
		} break;
		case INTERNAL_IMPORT_CATEGORY_MESH_3D_NODE: {
			const bool generate_physics =
					p_options.has("generate/physics") &&
					p_options["generate/physics"].operator bool();
			if (
					p_option == "physics/body_type" ||
					p_option == "physics/shape_type") {
				
				return generate_physics;
			}
			if (p_option.find("decomposition/") >= 0) {
				
				if (generate_physics &&
						
						p_options["physics/shape_type"] == Variant(SHAPE_TYPE_DECOMPOSE_CONVEX)) {