The article addresses this at the end. In software, the "times" do not move on like an unsteerable force. We (users and designers) decide how the times should move on. For non-mobile, the ≡ for menu seems like a step backwards and we shouldn't accept it without complaint.
Applying mobile patterns which are suboptimal on the desktop seems like a UX antipattern to me. I think a huge part of the problem is that software -- both free and nonfree -- needs to show "change" in order to signal it's still alive and maintained, but change for change's sake can be a bad thing, especially if you already had a pretty good (or consistent) UI.
I run Trinity Desktop on Linux for exactly this reason: it's basically what KDE 3 looked like 10 or 15 years ago. I run it so I don't have to re-learn all my workflows every time somebody comes up with some new eye candy.
I'm ok with three-dot menus on mobile, especially for features like "settings" that I don't use all the time - Whatsapp's dots menu works for me.
Using a dots/hamburger menu on desktop is lazy, I'd agree with you there; using it on desktop for things that people do use a lot like the editing menu in a painting program is atrocious.
When I DO need to bring up the menu, I'm usually one to two clicks from where I need to go.
When a hamburger menu encompasses the whole UI (metaphorically speaking) I'd definitely agree it's problematic-- and the same goes for random placement of menu items into a hamburger menu. That's just lazy design.
IIRC at some point in Opera, you could move the top-level menu into the hamburger, but it was still the same top-level menu as before. That would be better.
I've actually seen applications where the first button on the toolbar is a hamburger menu and when you click it you get a dropdown with File/Edit/... etc options, that work as expected. I can live with that for now.
So instead of just having File/Edit/etc. on the toolbar they're nested inside another menu? This seems like introducing an extra click for no reason :(
[EDIT: probably more than 90% of the time, actually; EDIT2: and I'm pretty sure there's an option to show a proper menu bar all the time for those that want it]