### Godot version

v4.0.beta.custom_build [0a9e6e478]

### System information

Windows 10, Vulkan, GTX 960 528.24

### Issue description

This [55420](https://github.com/godotengine/godot/issues/55420) issue seems that it is not completely solved since in the advanced importer the same thing continues to happen.

### Steps to reproduce

- Put a 3D model on the scene
- Open the advanced import
- Disable Auto LOD or whatever you want to change
- See how mesh doesn't change

### Minimal reproduction project

N/A
if (err == OK) {
			if (importer->get_save_extension().is_empty()) {
				
			} else if (import_variants.size()) {
				
				for (const String &E : import_variants) {
					String path = base_path.c_escape() + "." + E + "." + importer->get_save_extension();
					f->store_line("path." + E + "=\"" + path + "\"");
					dest_paths.push_back(path);
				}
			} else {
				String path = base_path + "." + importer->get_save_extension();
				f->store_line("path=\"" + path + "\"");
				dest_paths.push_back(path);
			}
		} else {
			f->store_line("valid=false");
		}
		if (meta != Variant()) {
			f->store_line("metadata=" + meta.get_construct_string());
		}
		if (generator_parameters != Variant()) {
			f->store_line("generator_parameters=" + generator_parameters.get_construct_string());
		}
		f->store_line("");
		f->store_line("[deps]\n");
		if (gen_files.size()) {
			Array genf;
			for (const String &E : gen_files) {
				genf.push_back(E);