Currently with "Loot scrolls" unchecked the bot doesn't pick up any scrolls regardless of what is set in "Keep this amount of scrolls" option.
The bot should pick up scrolls even if the "Loot scrolls" option is unchecked (temporarily override "Loot scrolls"), until the amount of scrolls to keep is reached.
That way you can leave "Loot scrolls" unchecked to save stash space, and the bot would still always have enough scrolls to ID items and create portals.
(If you wanted to never pick up scrolls no matter what you'd have to leave loot scrolls unchecked and set "Keep this amount of scrolls" to 0.)