arduino due bootloader

Hi Arduino Programmers,

As you might know, the arduino Uno optiboot bootloader code causes the led light to flash and also the sclk line to go high during code upload.

To turn off pin 13 flashing led in the opitboot code, I had commented out the line for pin 13 in the bootloader code and burned loader in Uno using ICP from Pololu.

Still sckl line goes high when code uploads.

Then gave up on using Uno and onto arduino Mega with its pin 13 used for PWM and thus ok to use sclk pin for SPI communication.

The Mega works fine as SPI master for communication with Altera fpga (a $20 dollar Cylcone II board) acting as SPI slave but needs a 5 Volt to 3.3 Volt translator. For this, a Gravitech 5V to 3.3 Volt adapter is used.

The question I have is that has anyone with experience using the Due with its 3.3 Volt logic levels notice issues with the sclk pin going high during code upload?

Perhaps someone might have used the Due in making a custom SPI interface for fpga or other devices.

Thanks in advance for your reply.

S. Fan