Connecting switch-mode supply negative terminal to Arduino GND
You are wise to be wary here.  You can connect them safely if you can be sure that the USB on your PC is tied to ground and you tie your power supply to the same ground, but if you are measuring a voltage between these grounds, your external supply must be floating. I would agree with you that you should not use the USB as your means of tying the grounds together, because the two supplies will float apart each time you disconnect the USB cable and you will get a spike or surge when you reconnect.  You would want to make sure that the grounds are always tied together through a separate path.  Unfortunately, you can's just tie your external supply to earth because PC USB grounds are not always tied to earth, especially when using laptops.

For safety, use opto isolators or similar between your arduino pins and other circuitry.