WingedKagouti: One thing I tend to do is make a large room that the NPCs can't reach, then place a bunch of chests as closely spaced as possible (using platforms). I also put down some Candles at regular intervals if the room is large enough to need lighting. This is mostly for mass storage of stuff that isn't immedately useful, such as vanity items, spare accessories, weapons, building blocks that I don't intend to use for crafting and so on.
I tend to place the most useful crafting stations in an easy to access area along with 2-3 chests (on platforms above the apropriate crafting stations) with the most common crafting materials (like metals, ores, and plants). That way I have easy access to whatever materials I may need and I won't need to run back and forth or search through a bunch of chests.
A chest for buff (and possibly healing) potions near your bed is a useful thing, if you've filled your piggy bank and safe with "I intend to use this for a specific occasion"-equipment. You may also want both a safe and piggy bank near your bed. Once again, my usual style is to put these on platforms above the location, this is mostly from pre-1.3 where NPCs were quite happy to spend an entire ingame day standing in front of a chest on the ground...
I made my floating workshop at 2-jumps height, now that I have a double-jump accessory. Even though a chair and table constitute a crafting station for a at least a couple things (watches, for instance), I'll have to remember to NOT put them in the shop lest an NPC decides to make it Home. For now, they won't be wandering in by themselves.
Currently, the chests are stacked 2-high, using platforms. I have around 16 now, with room to easily drop in another 8. About half are completely empty but I have yet to move stuff from the original chests in the house. Figuring on using one chest just for dirt and another for stone. I'm a hoarder, but am doing my damnedest to be an
organized hoarder. Haha
It was considered to group chests near specific crafting stations but then I figured that some materials can be crafted on more than one station, so I then dithered over how to organize THAT. But now that you mention it, there's no point putting dyes and dye-making materials in with the other chests, since you use them (almost?) exclusively with one station. Maybe I need to filter out those more-limited materials and re-jigger their placement.
One thing I do like is that you can craft directly from your storage chests, so long as it's within the proximity of the crafting station. I suppose this goes back to your suggestion... Now that I think about it, there's nothing preventing me from having, say, multiple workbenches, if that's what it takes to get the materials better organized and eliminate a bunch of running back and forth.
On the bed and potions... I'm not yet using a bed, but have been thinking about the possibilities. For now, at tinyE's suggestion (has that phrase EVER been used before? XD ), I did make a little building around my standard spawn point, and am thinking about putting a weapons-and-potions chest there in the event that I croak and need to go find my death loot. May as well get all of that stuff gathered in the place where I'll most need them.