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Unfortunately, any customization or changes to the Edison’s u-boot or kernel are not supported. I have found this thread that maybe can help you if you want to customize u-boot: https://communities.intel.com/thread/107935.
According to your issue, maybe you can create a script that changes the GPIO configuration when it is booting, to do this use this thread as a reference: https://communities.intel.com/thread/111545, but it I think you will have the same problem with the pin, or you can use another pin to avoid this issue.
I hope you find this helpful
Have a nice day.