Alice is still active in London when in her Wonderland state. What she was doing in Wonderland, she was doing in London at the same time - thus getting her to places she wouldn't have gone before.

We know this because in American McGee's Alice, when Alice is fighting the duchess, she's actually fighting a nurse in Rutledge Asylum who is trying to bathe her: Nurse D-.

She possibly fell off a bridge or something that got her into the water, got tied in a group of fisherman's nets and then was taken above the water before she totally drowned. Then when they got back to the dock, they noticed they had taken her aboard with the fish. That's the most logical way of putting it.

Well, this theory is certainly right when it comes to fight with Doolmaker. Alice is probably talking with Bumby and fighting with Doolmaker at the same time. In general, she's just standing in front of Bumby, so she doesn't have to divide attention that much.

But getting from rooftops to river seems to be very hard, when her mind is in Wonderland at the same time. I think that in this case she was simply fainted, because her deeds in Wonderland were to intense to focus on moving around London.

Also about Duchess. Yes, it's pretty obvious that she's Wonderland manifestation of Nurse D-. Yes, Alice called her "Duchess". But it could be in the early years of Alice's "stay" in Rutledge Asylum (although Alice spend here almost ten years). Maybe she called her "Duchess" simply because she was probably similar to her in some way.

I always thought that during Alice's adventures in Wonderland (in American McGee's Alice) she was lying still on her couch being in state of catatonia.

The boss battle simply represents her fighting with Bumby verbally and what she is feeling and thinking in her own mind during the time. If you've seen the beta trailer, Alice can move very swiftly around London. Some wooden floors break under her leaving her falling to grounds below - making it easy for her to move about.

"The boss battle simply represents her fighting with Bumby verbally and what she is feeling and thinking in her own mind during the time"

Well, that's simply what I'm thinking in general about this fight.

The trailer is very interesting.

"Some wooden floors break under her leaving her falling to grounds below - making it easy for her to move about"

Hmm... my interpretation is as follows: the first bridge-like thing collapsed for real. Then Alice is falling onto stone floor under it. And in my opinion, since stone floor must be really hard, Alice fell onto it and she lost her consciousness. But from her point of view she broke the floor and dropped into Wonderland.