Anyone that moves around a fair bit in this game keeps his/her toolbox as small as possible for transport (mine's a four-layer, six-drawer chest + what's under the lid). There's no way I could keep the same box if every tool had to have its own personal cut-out. To start with, I've got around a dozen punches of various sizes and shapes, ten rivet snaps, assorted reamers and some stepped cutters in one small drawer alone. I'd need three times that space if they had to be 'allocated'. And as for the spanners...
It's still down to disciplined area inspection in my opinion.
You could just as easily leave pens, redundant hardware or your glasses case somewhere and there's no control on them. I once saw a u/s vacuum pump left between the cylinders of a cowled-up engine and a batch label still taped onto the inner tube when doing a tyre change.
