### 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)
} else {
		file->store_32(count); 
	}
	for (const KeyValue<String, List<String>> &E : p_props) {
		for (const String &key : E.value) {
			String k = key;
			if (!E.key.is_empty()) {
				k = E.key + "/" + k;
			}
			Variant value;
			if (p_custom.has(k)) {
				value = p_custom[k];
			} else {
				value = get(k);
			}
			file->store_pascal_string(k);
			int len;
			err = encode_variant(value, nullptr, len, true);
			ERR_FAIL_COND_V_MSG(err != OK, ERR_INVALID_DATA, "Error when trying to encode Variant.");
			Vector<uint8_t> buff;
			buff.resize(len);
			err = encode_variant(value, buff.ptrw(), len, true);
			ERR_FAIL_COND_V_MSG(err != OK, ERR_INVALID_DATA, "Error when trying to encode Variant.");
			file->store_32(len);
			file->store_buffer(buff.ptr(), buff.size());
		}
	}
	return OK;
}
Error ProjectSettings::_save_settings_text(const String &p_file, const RBMap<String, List<String>> &p_props, const CustomMap &p_custom, const String &p_custom_features) {