I don't think it's the resource cost, but I think in my world that's certainly a factor since I can't seem to find enough surface deposits. Rather there seems to be a lot of one or two things that like to clog the chests you throw down. Dirt, peat, etc. It's pretty convenient to not have to look through chests too, as you can just hover and click with an empty hand and grab what you need. I honestly prefer the crates to ground storage for stuff like charcoal and peat and wood.
Since you have expressed a JIT style of play where you try and only spend time doing something when you need it, you obviously would prefer chests over crates. Besides that you can combine two chests into a trunk and get another 4 slots in a 2x1x1 package which is also pretty good storage economy. I personally do a lot of chore work at the start of each day. Shaving trees/bushes, harvesting grass, chopping trees. Stuff like that goes really well into crates and just comes out when it's needed.