I've dealt with this situation before, all too often. When I moved back in with sis about 9 months ago, we agreed that I would get the biggest bedroom with ensuite toilet and she would get the other two bedrooms (her and Sproglet) and we'd split rent in half. But when we lived together before that, she got the master bedroom (with ensuite toilet) and I'd get the second bedroom and we'd still split rent in half.
From what I've seen, if three people are living somewhere, no matter what size the bedrooms are, they all pay equal share of the rent. I was in a house in college. It just so happened that I moved in when someone was moving out of the master bedroom, so I got it. Okay, that's definitely nice. I was living with a guy, another guy moved in to the third bedroom. We all split rent equally. But original guy who had stayed had all of his stuff set up in the small bathroom. He didn't want to relocate to the master bath, and the other guy who moved in didn't feel comfortable sharing a bathroom with a girl, so I also got the master bathroom to myself. Excellent. Here's the thing, I didn't pay a dollar more for rent or bills than those guys did even though I had the biggest bedroom, the biggest bathroom, the only bathroom to myself, and the only bathroom with an actual bathtub as opposed to a shower stall. There was NO difference because it was agreed to, it was basically part of the terms of living together.
I think your DD needs to talk with her friends and see. You said it was already agreed that one girl got the master bedroom. Why is that? Is she willing to pay more already, so she gets the bigger space? If none of them are actually willing to pay more than the other, then the two girls will have to decide for themselves how to fairly decide who gets what bedroom, but I don't think an unequal rent split is a good way to do it.
I've also seen some ideas on switching rooms at semester. That's just a pain. It means you can't really unpack fully because you'll basically be moving again when the semester is over. And it's not just switching rooms, it could be clearing a space in the shared area to empty one bedroom out, move the other bedroom's contents into the empty one, then move the first bedroom's contents out of the shared space, then rearrange the shared space again. Too much of a hassle, to me. If I get a bedroom, I'm staying there.
Then again, I don't mind being in a tiny room, I don't have much by way of furniture or belongings, and I can easily sit on my bed to entertain myself or study or do homework. I expand into the space given to me, but don't generally overflow.