how to handle GND reference in Arduino connected to separate electronics?
You are correct, the Arduino ground and USB connector ground ARE connected. If the USB cable is connected to something grounded like A PC, then there will be a ground path through that. If your other electronics have their own ground path (you can test with a multi-meter), then you've created a ground loop. This may or may not be a problem, but it's best to avoid if you can. A simple way to fix this is to isolate your USB connection, so that the system has only one ground.

You can use a device like this:
https://smile.amazon.com/Isolator-Protection-Isolation-ADUM4160-ADUM3160/dp/B06XB9YBHJ

Or an IC like this one: https://www.digikey.com/product-detail/en/analog-devices-inc/ADUM3160BRWZ-RL/ADUM3160BRWZ-RLCT-ND/3897186

Some symptoms you might experience if you have a ground loop problem are glitches and dropouts of the USB connection.