(I will also say that macOS's menu bar app buttons were not designed with focus follows mouse in mind!)
Except for "natural clipboard support" (dunno what you mean) and "Emacs" (I am a vim user, so I set up vim shortcuts) I have everything you said in my i3 setup, however for every application instead only for terminal.
I'd assume the author means the same shortcuts as every other app, which would be Ctrl-C/V on Linux. Obviously that wouldn't work in the terminal emulator, but I don't see why you can't remap it to Meta-C/V (as MacOS uses) for that.
You could even remap it globally: http://askubuntu.com/questions/102846/remapping-keyboard-sho...
Pretty sure that has to do with you being used to different keyboard shortcuts, not with any inherent properties of the terminal app. I'm currently experiencing this the other way around (working on OS X being used to Ubuntu), and struggling with it as well.
The next screen is my editor, next browser, finally email/comms. ConEmu is OK on windows, and I've tried a few different linux terms, but not is as easy/nice to use by a mile.
"I’ve also run various Linux distributions and BSDs since around 2000, so am quite familiar with them"
Therefor i consider, it is not even a switch just more dedicated usage. Clickbait blogpost, if you ask me.
Most likely (hopefully, if you have a big powerful workstation) you use at least some big fat desktop application such as XCode, Visual Studio, AutoCad, Photoshop, Chrome, Mathematica, Office, ...
Just pick an operating system that works well with your hardware and your big fat desktop applications. All that terminal stuff will likely run anyway.