### 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)
while (true) {
		assign = Variant();
		next_tag.fields.clear();
		next_tag.name = String();
		err = VariantParser::parse_tag_assign_eof(&stream, lines, error_text, next_tag, assign, value, nullptr, true);
		if (err == ERR_FILE_EOF) {
			
			
			_convert_to_last_version(config_version);
			last_save_time = FileAccess::get_modified_time(get_resource_path().path_join("project.godot"));
			return OK;
		}
		ERR_FAIL_COND_V_MSG(err != OK, err, "Error parsing " + p_path + " at line " + itos(lines) + ": " + error_text + " File might be corrupted.");
		if (!assign.is_empty()) {
			if (section.is_empty() && assign == "config_version") {
				config_version = value;
				ERR_FAIL_COND_V_MSG(config_version > CONFIG_VERSION, ERR_FILE_CANT_OPEN, vformat("Can't open project at '%s', its `config_version` (%d) is from a more recent and incompatible version of the engine. Expected config version: %d.", p_path, config_version, CONFIG_VERSION));
			} else {
				if (section.is_empty()) {
					set(assign, value);
				} else {
					set(section + "/" + assign, value);
				}
			}
		} else if (!next_tag.name.is_empty()) {
			section = next_tag.name;
		}
	}
}
Error ProjectSettings::_load_settings_text_or_binary(const String &p_text_path, const String &p_bin_path) {