A month later update: For a few days, it continued. I'd separate them like a time out for a few minutes, letting the "dominant" one run in the ball, so the smaller one got time to himself in the box.
Whilst I wouldn't recommend it to anyone, as it's a judgement call for the individual, the "time outs" do seem to have worked (even though I know the hamsters won't understand it much, if at all). They're now both a similar size and I very rarely hear any squabbling, during the day or night (someone is nearly always in earshot) and they haven't had to be separated in over two weeks
They are still getting on well; grooming each other, sleeping together and sleeping separately, sharing things, etc. They'll stay together for as long as this continues. They'll be separated if it starts happening again because that will be a pattern.