This klipper configuration uses pin aliases. See below for the menuconfig options that worked for me.
The Eagle can be flashed with make flash FLASH_DEVICE=0483:df11 if you hold the BOOT0 button while it's powering up. Otherwise, you can also flash the Eagle via microSD card or USB drive. MBR partition table, FAT32. Make sure to name your new firmware image mks_eagle.bin or else it won't flash.
The Robin Nano V3.1 cannot be flashed with make flash but instead requires you to flash via microSD card or USB drive. MBR partition table, FAT32. Make sure to name your new firmware image robin_nano_v3.bin or else it won't flash.