When you enable the massCraftSwapsOnly option and press the massCraft key, only items in the inventory will be automatically crafted, not items in the backpack. The reason for this is that in 1.20.4, when using the swap method to craft items, only items in the inventory or a sidekick can be swapped.

the following is related code in ScreenHandler.internalOnSlotClick
if (actionType == SlotActionType.SWAP && (button >= 0 && button < 9 || button == 40)) {