One difference I noticed just now is that in my border layout with a west panel (with split: true) and my center panel the resizer splitter is a child component of the parent container with the border layout.
In 4.0.7 I would use westpanel.nextSibling() and would get the center panel. Now doing that I get the Ext.resizer.BorderSplitter.
Not a bad thing really, but was something that I had to refactor to get 4.1 beta 1 to work in my particular app / layout so more just FYI to peers.
The 4.0.x Border layout had all kinds of horrible stuff in to attempt to show the illusion of Ext 3.x where the siblings were just the actual configured child items - the regions. The splitters were hidden.
I think it's better now, you get a true view of the Container's items.
You can use a ComponentQuery selector on the nextSibling() call.