The engine mode 4 is just to replace everything with one block like stone so it appears to be absolutely nothing

You are basically describing engine mode 1. The reason you can still see blocks in engine mode 1 is that ores next to air can't be replaced with stone, otherwise legit players wont be able to see exposed ores either. To hide all ores an approach like #16 is required, which is rather complicated and computationally expensive!