### 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 (mesh_settings.has("lods/normal_merge_angle")) {
						merge_angle = mesh_settings["lods/normal_merge_angle"];
					}
					if (mesh_settings.has("save_to_file/enabled") && bool(mesh_settings["save_to_file/enabled"]) && mesh_settings.has("save_to_file/path")) {
						save_to_file = mesh_settings["save_to_file/path"];
						if (!save_to_file.is_resource_file()) {
							save_to_file = "";
						}
					}
					for (int i = 0; i < post_importer_plugins.size(); i++) {
						post_importer_plugins.write[i]->internal_process(EditorScenePostImportPlugin::INTERNAL_IMPORT_CATEGORY_MESH, nullptr, src_mesh_node, src_mesh_node->get_mesh(), mesh_settings);
					}
				}
				if (bake_lightmaps) {
					Transform3D xf;
					Node3D *n = src_mesh_node;
					while (n) {
						xf = n->get_transform() * xf;
						n = n->get_parent_node_3d();
					}
					Vector<uint8_t> lightmap_cache;
					src_mesh_node->get_mesh()->lightmap_unwrap_cached(xf, p_lightmap_texel_size, p_src_lightmap_cache, lightmap_cache);
					if (!lightmap_cache.is_empty()) {
						if (r_lightmap_caches.is_empty()) {
							r_lightmap_caches.push_back(lightmap_cache);
						} else {
							String new_md5 = String::md5(lightmap_cache.ptr()); 
							for (int i = 0; i < r_lightmap_caches.size(); i++) {
								String md5 = String::md5(r_lightmap_caches[i].ptr());
								if (new_md5 < md5) {