After making some research about what this NT stand for, I found that it is used for connecting two different nets to each other like analog ground and digital ground and since I am using Eagle, I wasn't able to understand what on earth this connection for(eagle does not have this specific Net tie thing)
I was confusing since in the SAM E70 Xplained dev board there wasn't anything like that but later when I went through the Duet3 Schematic I found they want to use the ref ground for specific tasks!
Anyway, releasing all the CAD file or at least the PCB layers in PDF format will be very nice to help people like me making their own custom board faster!