Several valid points are brought up... having the tool where it is needed is important. Aboard our 40'er we had a couple of wrenches (one was notched for impeller removal) down where they were needed. These items were tied to the bulkhead using 1/8" braided line.
If you are like me you will find several items become your Go-To tools. For instance, aboard Seaweed many projects can be solved by using these few tools: Phillips and standard screwdrivers, a small set of sockets and ratchet (1/4" drive), vise grips, a knife, wrenches, multimeter and infrared thermometer. My neighbor can't manage without his adjustable wrench (for me it's the vise grips)
Those items will need to be easily accessible.
As for your tool chests and such w8n4sun... well, I don't know that I would want to have metal tool boxes due to the rust factor. Even if your boat is perfect, the salty environment can wreck havoc.
A 36'er I worked aboard last year had one large battery box for the engine room tools. That was handy, having them all organized in one spot.
Mine are scattered. One locker has the most frequently used items. I had the end cut out of one of my dinette bench seats so that I could access the locker without moving the cushions. It's easier.
The inside:
Sure, it would be nice to have matching plastic containers. For now though, this works well. Calder's is just to the right, with further back there two plastic folders filled with the paperwork from my gear.
The paperwork is sorted, alphabetically:
Whatever your setup becomes w8n4sun, I have never heard any larger boat owner regret having a permanently mounted bench vise. If you're really lucky a bench grinder can be a nice addition too. All the best to you.
Happy Boating.