Hi vanessa_dis,
Sorry for let you misunderstand me.
No, I don't mean that the changing GPIO has more priority than boot mode in the serial downloader.
let's know how to enter the serial downloader mode at first, just when you configure the BOOT_MODE[1:0]=01, then POR or reset happens you will enter the serial download mode, please note, in the serial download mode, customer can't control the pin functions directly, as the ROM already configure it, your PC will still can recognize the USB HID, then you can use the USB HID to download the app code. But if it is the internal boot mode, I main, you already enter the internal boot mode, then the pins, even the BOOT_MODE pins can be controlled by the user. So you can use the app code to change the pin function or even try to disable the USB clock, eg, CCGR6[CG0].
In conclusion, during the reset which will select the boot mode, external related pin signals will determine the boot mode, and in serial download mode, you can't disable USB, in internal boot mode, you can control the code to change the pin mode.
Wish it helps you!
If you still have questions about it, please kindly let me know.
Best Regards,
kerry