This has been a known quirk of the crafting system for a long time, one that we cannot readily solve currently (though we are still looking for a solution). It's the same issue as chitin plates that need to be taken off the woodworking table then placed back on it so they may be used.
In the meantime the bundles still remain useful, at least allowing for bulk buying supplies, and to quickly remove supplies that have not been used from the crafting stations. It's half what we want it to be, but a definitive quality of life improvement anyway.