There is a command line flag but it isn't exposed in the RetroPie-setup script -mame_img and -console_img These accept an ordered list of image preferences which RetroPie-setup sets to -mame_img="t,m,s" and -console_img="b" So the order is Title, Marquee, Snap for mame. You can exit EmulationStation and run this from the command line with something like this but cd to the rom folder you want to scrape.
cd ~/RetroPie/roms/mame
/opt/retropie/supplementary/scraper/scraper -mame -mame_img="s,t,m"
More detail about all the flags is at
/opt/retropie/supplementary/scraper/scraper -h