All the augments will go through walls after the winter update. If this is intentional then so be it but it wasn't easy to get the augments in the right place and use them in the first place. If this is intentional it won't be worth crafting anything using them due to the hassle.
Hi! If you hold E and select "Inspect" on a crafting station, this should open the augment menu, allowing you to pick and choose which augments are applied to that station