Because you can repair it with cobblestone instead of sinking a Modifier on Flux or Repair.
The flaw in that logic, the tool is inherintly slower than the more advanced tool. So the first modifier may be lost just in playing catch up to the better tool. Also you have to switch tools every time you want to mine something like redstone (which I want to silk touch anyways). Tool switching costs time which is like losing a modifier to speed again.
Though early game, stone tools are the best I agree.