### Godot version

4.1 24cb43a

### System information

Windows 10 x64

### Issue description

Every time I launch Godot, I'm greeted with this in my console:
```
ERROR: Resource file not found: res://InputEventKey_7cuxk.
   at: (core\io\resource_loader.cpp:227)
```
Seems to be only happening in Project Manager and comes from this:
![](https://chat.godotengine.org/file-upload/udqZP8NQfogp4rjRL/Clipboard%20-%2021%20kwietnia%202023%2022:24)
It's part of my `editor_settings-4.tres`. I didn't test, but I think it applies to any shortcut that you customize. For some reason ResourceLoader tries to load it as a project resource, while it's a sub-resource.

Does not happen in 4.0.2.

### Steps to reproduce

1. Open Godot 4.1 project manager
2. Check the console

### Minimal reproduction project

N/A
* The initialization is typically done in 3 steps (with the setup2 step triggered either
 * automatically by setup, or manually in the platform's main).
 *
 * - setup(execpath, argc, argv, p_second_phase) is the main entry point for all platforms,
 *   responsible for the initialization of all low level singletons and core types, and parsing
 *   command line arguments to configure things accordingly.
 *   If p_second_phase is true, it will chain into setup2() (default behavior). This is
 *   disabled on some platforms (Android, iOS, UWP) which trigger the second step in their
 *   own time.
 *
 * - setup2(p_main_tid_override) registers high level servers and singletons, displays the
 *   boot splash, then registers higher level types (scene, editor, etc.).
 *
 * - start() is the last step and that's where command line tools can run, or the main loop
 *   can be created eventually and the project settings put into action. That's also where
 *   the editor node is created, if relevant.
 *   start() does it own argument parsing for a subset of the command line arguments described
 *   in help, it's a bit messy and should be globalized with the setup() parsing somehow.
 */
Error Main::setup(const char *execpath, int argc, char *argv[], bool p_second_phase) {
	Thread::make_main_thread();
	set_current_thread_safe_for_nodes(true);
	OS::get_singleton()->initialize();
	
	
	OS::get_singleton()->benchmark_begin_measure("startup_begin");
	engine = memnew(Engine);
	MAIN_PRINT("Main: Initialize CORE");
	OS::get_singleton()->benchmark_begin_measure("core");
	register_core_types();