Mostly a subjective topic, *VERY* YMMV.
Prettier/better girls at Club? Tell that to Rebecca, she and Yuzu are my absolute top 2. Tiffany used to be my top. Rebecca and Tiffany seem permanently at 479, Yuzu recently moved to Club.
From chatting with loads of girls, it seems to be an offer made to them where they get their own room and choose their own rates, but will get less traffic, especially in terms of line-ups.
Some girls want that extra comfort, some stay with the extra business. Depends on them.
479 also only charges more than the default $140/30min seemingly based on freshness; typically, very new, young Japanese girls get that extra price tag. Other factors are sometimes involved, too, it just appears that the management predicts popularity due to certain qualities and throws a bit more on for the girl's benefit.
I will say though, I definitely agree with the whole thing about errors in room allocation; my one and only case being at 479, where reception messed up and sent my booked girl to a lineup while I was in the waiting room. She went up to the room, I was forgotten, and when I asked, they were noticeably confused and sent me to an empty room, nearly knocking down her door thereafter to reassign her.
It was a busy day, I don't blame them. I just wish they'd admitted to the fault and not stressed her out so much.