This is currently working as intended. The "fill from backpack" option is so you don't have to drop 20 dyes into the trade crate and such. Since stackable objects come in one neat package, there's really no need for that. It's also much more complicated to process a stack of objects into the crate vs. a single object when we're dealing with automation, hence the stackable items will not fill from the backpack. That option will also ignore insured items in a future update, to reduce the likelihood that your crimmy will get pulled into the crate when it's asking for half aprons.