I might be understanding you poorly here...
The author is not dismissing this in the sense of saying “it's impossible and that's okay” but rather “it's possible and it never generated the ambiguity in the first place, so it needs no special logic.”
So you probably actually use undo-redo in two big ways:
1. I just pasted the wrong thing or modified the wrong file or the kid grabbed the keyboard etc, I want to quickly erase N changes.
2. I want to grab info from the past and surface it back to the present. I cut something and then lost my clipboard contents, or so. This is what you described.
The problem in the article is, basically imagine that you get the key wrong. You do your browsing thing, you are N levels back in time, but instead of Cmd-c to copy this block of code, you accidentally either Cmd-x which deletes it, or Cmd-v or Opt-c or so which overwrites it. You were trying to do (2) but now the dominant heuristic suggests to the computer that you are actually doing (1). Because in the usual implementation of undo-redo, undos push changes off the history onto a stack, redos pop changes off the stack onto the history... And any new change clears the redo stack! That stack clear is the heuristic providing the difference between (1) and (2). When the heuristic misfires, it misfires in really dangerous ways, potentially eating hours of work.
So (2) is not being dismissed as “who cares” but rather as “that's fine because our heuristic has not yet led us astray, every implementation of undo that has redo will solve obvious-(2) and obvious-(1) correctly.”
This is where I might be misunderstanding you, I am not clear if you are saying that your editor is cooler than this default interpretation in some way that does not require “redo all the way back and cut-and-paste the previous partial state”...? If so then I would have to hear more before I could know if the article’s “history is always chronological, but browsing history is different than undoing it: undoing it only happens on an edit to an old browsed copy and saves a history-rollback into the modern chronological history, rather than fussing with undo graphs or whatever” approach works that way.
Edit: actually, the article’s approach of having a browse mode solves your problem automatically in a counterintuitive way... Cut instead of copy, you will get launched out of browse-mode, then undo twice to get to the tip of your history. Counterintuitive but definitely saves some keystrokes.