For various reasons, most Linux applications try not to use the Super (Windows) key for anything by default, which makes it a good candidate for use as a custom modifier key for whatever you want. For example, users of tiling window managers often use Super+... for interacting with their desktop (open a terminal, open a launcher, switch workspaces, swap windows, etc.).

There's nothing stopping you from deciding to use Super+c/v as copy/paste instead of Ctrl+c/v or Ctrl+Shift+c/v. Apple doesn't use Ctrl+c/v either... they use Command, so the conflict you're referring to doesn't exist there either.