I don't think public multiplayer games are a priority in general. Factorio is a very popular game for it's type (last I heard there were maybe around 2 million copies sold?), but look at the multiplayer server list and there's maybe 100 people in public servers and another 50 in passworded games on ...

This doesn't seem like an issue with the game/server software. It's an issue with someone doing some kind of denial of service attack on the server. Doesn't seem to be much you can do until they get bored and knock it off (or you block every single IP they're using, which can be a monumental amount ...