It's not as simple as swapping the keys. On macOS you use the "win key" for system shortcuts but you can also use the Ctrl key for emacs-style movement systemwide.
For example I can type Ctrl-b while editing the URL in the browser omnibar to move the cursor back a character or alt-b to move it back a word, just like you can in the terminal and then use "Win"-b to bookmark a page.
And your command changes the keys you use for moving the cursor in the terminal.
In GTK2 and 3, you can switch to the emacs key theme and then edit the files in /usr/share/themes/Emacs/ to have meta instead of ctrl. Alternatively, use a key rebinding daemon like https://github.com/snyball/Hawck to rebind the specific keys globally. Long-term I don't think this is worth it though because the programs are not built to support it like they are on a native Cocoa environment. You kind of just have to suck it up and get used to different key bindings in different environments.
No one wants to fiddle with keybindings. Occasionally using Ctrl-c in the terminal (which forces me to redo my text selection or worse) or Ctrl-Shift-c in the browser (which brings up the dev tools that I have to close with Ctrl-Shift-i) is just the cost of using Linux.
MacOS's system is a better system that will never be adopted because there no will (just suck it up as you say), market pressure or authority that would impose it.
Well, that's not the cost of using Linux. It's one possible cost. I haven't ever done either because I use the primary selection (select is automatically copied, middle click dumps it at the pointer).
And when I can't or don't want to do that, I right click and choose Copy.
If I want to use another operating system - Windows or MacOS, it drives me batty that I have to keep going around copy pasting things.
I tend to agree with you that having a difference between Ctrl and Command is nice. But it doesn't actually solve the problem - it works _because_ MacOS is a minority, the last holdout.
In your web browser, Cmd-A will select all the available text but Ctrl-A will move your cursor to the start of the line. In your terminal, perhaps Cmd-A will select all the visible text but Ctrl-A will increment the number under the pointer (since you're running VIM in it).
If the Meta key hadn't died of death and Linux developers had kept expecting it to be around, there could also be clashes between Cmd and Meta.
You (yes you) could patch the toolkits to do what you want right now, all the code is free and open source. But if you lack the will to do it, and see it as unimportant in the grand scheme of things... well maybe that's an indicator that the keybindings really aren't that much better and are mostly up to a matter of taste. I personally don't really care much for "market authorities" trying to force me to do things.
The one that gets me every day is ^W — erase word — against the handful of programs that refuse to let me configure that away from ‘close window’ (I'm looking at you, Chrome).
For example I can type Ctrl-b while editing the URL in the browser omnibar to move the cursor back a character or alt-b to move it back a word, just like you can in the terminal and then use "Win"-b to bookmark a page.
And your command changes the keys you use for moving the cursor in the terminal.