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.