We were thinking about changing alpha instead of changing size, but in general, that's a harder solution to perfect out. For example, someone might leave the patch uncleared. If it does have a low alpha value, then the player might not be able to see the patch again. With a small patch, it still will be clear enough.
Plus, I think changing the alpha channel on one material (out of all) would break the instantiating which would be slightly worse for the runtime performance. We wanted to bring this game on WebGL (on which we are still slowly working and getting great progress).
Thanks for playing! I've reviewed your game too!