I don't recall what problem I had with it, but it was a case of solving one problem and introducing another.
I don't want to globally swap Ctrl and Cmd. For some apps, the keys are identical to that on Windows. For others, it isn't. I need to be able to do it on a per app basis.
I assume the problem would be in the Terminal (assuming you use it), where Control + C is an often used shortcut, and flipping the modifiers globally would make this Command + C.
macOS uses Command instead of Control for a lot of things, but they didn't change how the shell works.