Using an old original disk will inevitably destroy the media.
Sometimes you are lucky if you have one chance to read out the content before the magnetic layer gets damaged.
This is especially annoying with rare and often expensive games; think about games published in 1984...
People buying and using original software for nostalgia's sake or collections are often not aware of the risk of constantly using an old disk.
Using media directly would definitely encourage destroying historical material this way and hence such use is not supported - please remember, our concern is software preservation and we won't make our work even more difficult and expensive.
It is supported to write back already preserved software to disk and you are free to use the new disk any way you like on the original hardware - as you say nothing beats the real thing
Have an idea how to make KryoFlux even better? Let us know...