You need to have MX31 silicon version TO2.0.1 in order to boot from SD/MMC.
There is Redboot support for booting from SD/MMC on MX31 (TO2.0.1) on Redboot 200841 and later versions. There is also a pre-built image that can boot from from SD (mx31_3stack_redboot_mmc.bin).
You can use ATK to flash this image into SD card.
Regards,
Fabio Estevam