The option, assuming it is still the same in the autopatching lines, merely prevents you from being able to cancel the save being written back. It will always appear unless you clear the RAM somehow (anybody that wanted this tended to remove power to the SRAM). It is necessary as that is how the saves work -- the games get patched to use SRAM, the cart provides SRAM and then copies that data to the SD card and back out before launching. You could change some of the pictures and text I guess.
The EZTeam might be able to code in a thing to hide said named folders (there are various things already which read extensions and do things accordingly), historically there was some reason to go into the SRAM one and patch is new.