Plenty of items are non-stackable, that you still want stored away. Like spell pages, advanced warfare thingies. Not that they should be like that, but janky stack sizes is the main reason to have dedicated chests for one type of item, and quicksort makes it more bearable.

The root issue is that CE lacks favorite tagging like in Terraria.

I would suggest having separate chests for things that don’t quick-sort properly. I usually quick-sort repair kits into my tinker’s, but if I wanted to carry kits on me, I would move any spares into my equipment chests by my bed, so I still could quicksort like before.