I have three kids and absolutely love my bunkhouse. I would recommend it to all parents.
She is crying coming back to you now, but next year, she'll be sleeping better in a TT and if she's sleeping in the main living area, you won't be able to move around without waking her. Who wants an unrested child? Nobody.
I love how my TT has a solid door for the bunkhouse. When I had a toddler, we could put her down for a nap and still use the rest of the TT while she slept. I could cook, watch tv, go in and out and she'd never know the difference. Our youngest is no longer a toddler at 6, but she still goes to bed way before anyone else. I know that she has a nice quiet place to get a good night rest while the rest of us continue to have a nice time and don't have to tip-toe around her afraid that she'll wake up.
Basically, it's just like home.
If you're not wanting to waste space, you can always use the other bunks for storage somehow. Maybe modify one with cabinets.
