If you want to use replaygain, you should probably use more modern software, otherwise you will need to script in figuring out what files are in what album.
According to the manual, if you don't specify anything, the values are written to tags but the files aren't modified.
Mp3gain probably doesn't even support EBU R128, right? I'd really wouldn't want to use it for scanning anymore.
The downside is that, even though Mp3gain claims it's lossless, it's not perfectly safe to ensure that an Undo-process will restore the waveform perfectly.
I don't care that much about 100% accuracy, as long, as the differences are not too great.