Well, then it's not a good design. It makes no sense on several levels.
First of all: There is no "main" window. Which one is the main? What features does it have that the duplicate does not?
Second: The bookmark implementation is chaotic.
1. If I open a document with bookmarks, then make a duplicate, the bookmarks are not duplicated. How is that a duplicate?
2. If I open a document with bookmarks, then make a dupicate, then create any bookmarks in the duplicate, then close the original, then close the duplicate, the bookmarks in the original are lost.
3. If I do the same steps as in #2, but do not make any bookmarks, then the bookmarks in the original are preserved.
If that's not error prone, I don't know what is.
Third: Any editing I do in either window is immediately inherited by the other. This should apply to bookmarks.
Fourth: If I have two windows open (a "main" and a "duplicate") and I enter some test in one and then go to the other, Undo will undo the edits made in the other window. That's not very independent.
Even your analogy breaks down. For one thing, no editor should allow me to open two independent instances of the same document. Imagine the errors if I can open instance A, open instance B, edit and save A, edit and save B, rinse, repeat. I contend that this should apply to any attribute of the document, such as bookmarks, since they are saved as part of the document.
The only thing that would save this illogical design is two save two sets of bookmarks and reopen both "copies" the next time the document is opened -- or ask the user what to do with the bookmarks.
I say it's a bug in either the implementation or the design.
I am running UE 126.96.36.1990 on WinXP (all updates applied).