EMI shielding ground and isolated DC/DC
My take on this: You have three GNDs:

External GND with an unknown amout of external noise, that's the GND at the input clamps
Non-Isolated GND, the filtered Ground before your isolated power supply
Isolated GND, the Ground after your power supply.

Especially the non-isolated / isolated GND mustn't mix, look at your isolation requirements to decide on a suitable clearance. External GND and Non-Isolated GND can be made the same, but when you do the layout, think of them as separate. Don't use the &quot;unfiltered&quot; GND front of the filter for anything, and route it with a lot of clearance to other parts of the device, you may have bursts on there.
EDIT:
OP updated drawings. Option 1 is now a Fill only around secondary side and Option 2 is a Fill around the whole PCB area, with Input area cut out, but no additional circuitry who uses the GND anywhere.
Option 1 would be my approach. To decide if Option 2 has any Use, more information is needed. If your design includes some antenna for sending, it may be beneficial to have a bigger GND pour, for better antenna performance. But that is some complicated stuff I won't go into now. Pour your GND where you need it and leave it out where you don't need it.