There are two cases where a “don’t craft” flag (or container?) becomes useful:
1) sorting the items with different criteria -> preference is lost
2) putting the item at the end of the list, then collecting more from the same type (e.g. branches) but they are not “exceptional”. If I want to keep the exceptional one I have to regularly move it to the end of the inventory or put away in a chest. (I was using this second option after playing enough to be able to build one.)
For newbies like me an Inventory -> Crafting highlight (same as already implemented in the other direction) would help a bit. So when I point to some items the recipes containing that ingredient could be highlighted. Not an issue initially but after a few hours of playing.
1.9.2 bug: when using zoom out from options, right clicks are broken afterwards. They are reporting sand instead of seaweed etc. Couldn’t figure out the offset or the factor how much it is off by though.