I think waiting till four weeks is to be able to sex them correctly
It might not be possible to sex them easily at three weeks - but I'm really not sure with dwarf hamsters (I know with robos it's usually at four weeks).
I think go with your gut. My only thought was it might be stressful for Gertie trying to monitor the babies if they are all over the place. They do generally all stick together around the Mother and she can keep an eye on them and nudge them into place etc. While not being able to do that might be giving her a rest, I guess it could be stressful in that she has just given up as they are all over the place. But perhaps there is no right or wrong way. Maybe ask Souffle?!
Who has had many litters!
On the plus side, the babies are learning independence quickly and exploring. I think the usual thing is - being around the Mother without much distraction, until they are separated into male/female groups together, then going into their own cage/set up with variety when they go to a new a home - ie the first bit of independence. And they're usually ready for that by 6 weeks.
I am just wondering if they are weaned yet or still feeding from her as well as eating? Google tells me that dwarf hamsters aren't weaned from the Mother's milk until three weeks.