### Godot version

v4.0.2.stable.official [7a0977ce2]

### System information

Windows 10

### Issue description

The settings found in **application/config/project_settings_override** end up being written to the `res://project.godot` every time the editor is started.

I find this inconvenient, `res://project.godot` is always on the changelist in git because of this.

I think it would be better if settings with the same value as found in **application/config/project_settings_override** were persisted in `res://project.godot` **only** when set by the "editor interface" or "by code" and not by the "merge" that happens at the start of the editor.

### Steps to reproduce

1. Before opening the MRP in the editor, note **window/size/mode** value within `res://project.godot`;
2. Now open it in the editor and check the `res://project.godot`, notice that **window/size/mode** was changed by the contents of `res://project_override.cfg` (which is the **application/config/project_settings_override** file).

### Minimal reproduction project

[Projects Override Merging Into Project Godot.zip](https://github.com/godotengine/godot/files/11555239/Projects.Override.Merging.Into.Project.Godot.zip)
Error error = save_custom(get_resource_path().path_join("project.godot"));
	if (error == OK) {
		last_save_time = FileAccess::get_modified_time(get_resource_path().path_join("project.godot"));
	}
	return error;
}
Error ProjectSettings::_save_settings_binary(const String &p_file, const RBMap<String, List<String>> &p_props, const CustomMap &p_custom, const String &p_custom_features) {
	Error err;
	Ref<FileAccess> file = FileAccess::open(p_file, FileAccess::WRITE, &err);
	ERR_FAIL_COND_V_MSG(err != OK, err, "Couldn't save project.binary at " + p_file + ".");
	uint8_t hdr[4] = { 'E', 'C', 'F', 'G' };
	file->store_buffer(hdr, 4);
	int count = 0;
	for (const KeyValue<String, List<String>> &E : p_props) {
		count += E.value.size();
	}
	if (!p_custom_features.is_empty()) {
		file->store_32(count + 1);
		
		String key = CoreStringNames::get_singleton()->_custom_features;
		file->store_pascal_string(key);
		int len;
		err = encode_variant(p_custom_features, nullptr, len, false);
		ERR_FAIL_COND_V(err != OK, err);
		Vector<uint8_t> buff;
		buff.resize(len);
		err = encode_variant(p_custom_features, buff.ptrw(), len, false);
		ERR_FAIL_COND_V(err != OK, err);
		file->store_32(len);
		file->store_buffer(buff.ptr(), buff.size());