I have verified on Windows 10 that if I start two separate instances of the IDE, changing the PORT number on one will cause the other's PORT number to change also. One is on PORT 31, the other is on PORT 21 (one is a LoRa Sender, the other is a LoRa Receiver, so I see in the title bar). This is just plain NUTS! The only conclusion I can draw is that these are NOT two separate instances, but are sharing some underlying information. I've used the same technique to open the second instance as I use to open multiple instances of Windows explorer - I right click the icon in the taskbar and then select the application name. It works for every other application I've tried on my computer, except the Arduino IDE.
I'm running Arduino.CC IDE version 1.8.5 which I believe is the latest.