This really needs an input from @reduz. Including module code in scene can be quite problematic.

@akien-mga told me that this core hack is a no-go. Closing.

To be clear, I said:

And yeah for #71004 the core hack is a no-go, we'll have to find a different solution. Can't this be handled in the GDScript resource loader, so it can fallback to the shallow stuff by itself?
Otherwise, if it's only needed for ResourceFormatLoader, then it will need more abstraction so that this can be configured from modules/gdscript. GDScript shouldn't escape its containment room 😈

I do believe that it should be possible to move this to GDScript code somehow.

Can't it be done here?

Ref<Resource> ResourceFormatLoaderGDScript::load(const String &p_path, const String &p_original_path, Error *r_error, bool p_use_sub_threads, float *r_progress, CacheMode p_cache_mode) {
        if (r_error) {
                *r_error = ERR_FILE_CANT_OPEN;
        }

        Error err;
        Ref<GDScript> scr = GDScriptCache::get_full_script(p_path, err, "", p_cache_mode == CACHE_MODE_IGNORE);

        // TODO: Reintroduce binary and encrypted scripts.

        if (scr.is_null()) {
                // Don't fail loading because of parsing error.
                scr.instantiate();
        }

        if (r_error) {
                *r_error = OK;
        }

        return scr;
}

Might require more work to figure out if it's failing loading due to parsing errors or due to cyclic dependencies (maybe this can be passed via err in get_full_script().

Can't it be done here?

No. :(

Considering that a.gd is the script of a.tscn:

1. a.gd loads by ResourceLoader::load()
2. ResourceLoader::load_threaded_get() checks if thread_load_tasks has a.gd. It has not.
3. ResourceFormatLoaderGDScript::load() runs on a.gd, calls GDScriptCache::get_full_script()
4. a.gd refers to b.gd
5. b.gd preloads a.tscn
6. a.tscn loads by ResourceLoader::load()
7. ResourceLoader::load() tries to load a.gd (again)
8. ResourceLoader::load_threaded_get() checks if thread_load_tasks has a.gd. It has.
9. ResourceLoader::load() returns a null res

ResourceFormatLoaderGDScript::load() is not called if thread_load_tasks has already a file.

Otherwise, if it was called, GDScriptCache::get_full_script() supports cyclic references.