I'm not sure I understand the correct order of routing & defining copper pours (particularly when the pour is on the GND net.
In the screenshot below, you can see a white trace connecting two pads that are (properly) connected to ground. Why the trace?
Should a copper area be defined before auto-routing or after?
You need to understand, the copper area net is GND, this track is GND, so they will not appear the clearance.
for your problem, you don't need to route the GND track, just copper pour with GND net will be good. The GND net will connect together.