This reads to me as the default behavior of "cut" makes certain usability choices that don't gel with the author's personal mental model and workflow, which is of course totally valid. But it is odd to see things described as a "flaw" instead of a choice.
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.
Yes, I disagree that the cited behavior is defective. But I respect his pointing-out of the shortcomings and offering other options.
I find myself using the clipboard-erasure "defect" somewhat frequently to cut something to the clipboard, and then undoing the change and using the clipboard contents. And this is specifically useful in a way that merely copying isn't... but at the moment I can't remember why, or whether I use this when programming or working around InDesign's many defects.