As of 1.21, it is still tedious, however, it is possible to use crates by holding the stack of grain in your main hand with the slot selected, open your inventory, then hold down cntrl, shift, alt, and then aim at the crate and "left click" as opposed to right click normally. This complication seems to be due impart to the function of placing/removing items from a ship via cntrl, right click. it needs an overhaul, but i do not believe it is likely to be reworked in the 1.22 release.