I was driving a relay from Arduino Uno R3 Pin 13. I observed that every time I upload some code the led on the board designating pin 13 would blink. I'm curious why this is so. I understand that the serial LED blinks cause there's a serial transmission but why an IO pin?
See What happens when code is uploaded using the bootloader? - the flashing is by design.
Probably the reason is to confirm that the bootloader has started.
It's driven by the bootloader, which is performing the flashing (I suppose you are flashing through the USB port).
To show that the bootloader is functioning satisfactorily to the hobbyist. Boot loader helps to upload new sketch on the chip.