Unfortunately this can't be avoided. I need to keep track of all the chunks in a list that I iterate through in steps. That list is pretty big if you have a big world. Getting rid of this list would mean a massive performance impact as that list would then need to be generated real time each time the mod does an operation.
If you have large areas on your map that aren't used you could opt to remove those chunks and thus reduce save time (it will take a full chunk cycle before Noxys Trees rebuilds the chunk list, which can take quite a while if you have that many).
