Not using the combination for one of its ambiguous purposes does not strip it of ambiguity, you've just trained yourself to avoid those circumstances.
That, of course, is one of the pain points that the article addresses: Training yourself to do so is additional cognitive load that never should have been necessary in the first place.
I flip between macOS and Linux and, occasionally, Windows. On one of my laptops, insert is also a Fn switch away, so I have to either remember that this machine needs Ctrl-Fn-F11 specifically when I'm copying from terminal.
On another keyboard I have the same problem, but insert is mapped to a different key entirely, so it is ctrl-fn-equals, and fn is on the opposite side of the keyboard from ctrl.
Contort my fingers in which way on which keyboard? Mental load and annoyance I don't need.
That’s a hardware problem. I avoid mental load and annoyance by using the same keyboard layout everywhere. Even on Windows the bottom left modifier keys on my keyboard are Ctrl Alt Win, and not Ctrl Win Alt.
The keyboard is the most important input device on a computer. It’s worthwhile to customize your key mappings to fit your muscle memory.