Is it possible in the Arduino sketch to upload a binary file into flash memory array at compilation?
I'm not entirely sure what you are asking. Do you mean "Can I compile a sketch then somehow send it to an arduino sketch that will store it into a flash array?" Yes, you could do that but there's no built-in easy way to do it. You'd have to code it all up. All the Arduino IDE can do is compile things and upload them as the main sketch.
I have a binary file on my PC. This binary file contains data that I want to put in a data array that could be use in runtime by the Arduino DUE.