In manufacturing this is often referred to as "Kaizen" [1], more specifically as 5S / "Seiton" part. There's even quite a substantial (though not cheap) market for kaizen specific foam inserts / foam sheets. Mainly these are easier to cut and have contrasting color for top and middle layers, showing obviously if a tool is missing from its place. Look up "kaizen foam" if interrested.
[1] https://en.wikipedia.org/wiki/Kaizen