I am generally messy when setting up, or working on a machine.
Tools all over the workbench - sometimes two workbenches or more, my mind takes a pic and I know where the stuff is. It's a mess while I'm working but I save time by not being quite so organized on the workbench.
When done, I will put the seldom used tools up...during the run and as I get time and get in the mood.
Often used tools are duplicated and kept at each workbench and machine.
Most tooling is kept directly on top of the lathes.
That's a good thing about the older generation Mazak CNC lathes that I run: they're not too tall! Perfect for inserts, allens, torx, chuck jaws, insert shims and screws, anti/seize, jaw bolts, calipers, mics, coolant fittings, chuck plugs, tool holder bushings...
Right there on top of the machine, easy to reach and fast to get.
I've still wasted a bit of time over the last couple of decades walking, and hunting shit all over the shop.
It is a lot of work keeping a working shop decently clean and organized.
We spend the time to keep the place relatively clean, regardless of money-making time lost. (A lot occurs while making money though...haha). Chips are always gotten up, and the outside of the machines are always clean!
But putting every tool back, knowing there's a high probability the next time you need the same damn tool will be at the same machine you're currently working at!
When deciding how neat you want to be, you have to consider the balance between neat and money-making time lost. At least in the small shop, where pretty much every hour counts.
ToolCat