Given an isolated DC/DC converter, such as Traco TMR4. The GND fill, and internal GND layer(s) would be referenced to the -Vout pin. The TMR4 has an application note showing a fairly typical EMI filter for this kind of components. (https://www.tracopower.com/sites/default/files/products/application_notes/tmr4_emc.pdf)
Should the section of the board that contains the EMI filter have a keepout for the GND fill (illustrated by option 1)? Or is is better to let the GND layer (and top layer fill - with appropriate clearance) cover the entire board (option 2)?
Blue layer is inner GND layer. (Illustration only, this is not the actual circuit)