I don't really know if I should open this in either Sophisticated Storage/Backpacks, as this is common functionality. I assume it's borrowed from the Core mod, so I'll go and do it here.
Could it be made that the "Transfer to Storage/Inventory" buttons (the Red/Green ones on any Sophisticated GUI) include the hotbar so it also transfers matching items from/to inventories matching the whole player's inventory? It could be used with a modifier key, such as Alt and leave the default Shift modifier to transfer all (extra points if it could be edited in the Keybinds menu if possible.