The most glaring example seems to be the first: typically an accidental cut was intended to be a copy, not a delete, so leaving the text in your clipboard is a sensible design. I understand the author's perspective, and maybe OSes should have configurable "cut." But I think most people understand "undo" as "undo change to file" and not "undo change to file + OS state." In that sense the default behavior is not a flaw.
Again - the author's points about an alternative cut are reasonable, but they seem to appeal to a minority of users.