I feel that this punishes people for not actively hunting the cells and not immediately going for a Zygarde Cube, with people making more and more dead chunks as they go and explore or hunt for the materials for the cube. Not having a cube and just exploring or hunting for other pokemon means you are 'killing' chunks. If the world has a limited size, like an Adventure Map, this means that there is an effective time limit on getting Zygarde at all, unless people confine themselves until a cube is acquired. While a Legendary should be hard to find and get, I don't feel you should be punished for not actively hunting it.
I propose one of 3 changes, if not going into the mod, to at least add to config options
1. Add a config option for the 'life' of a chunk, meaning chunks can be loaded for more (or less) time before they are dead regarding spawning cells.
2. Lets chunks 'recharge', so that after a period if time of not being loaded they can once again spawn cells.
3. Let Zygarde cells be seen and collected without needing a cube, but needing a cube to properly store the cubes for use with the Reassembly unit.