When something doesn't make sense, look for answers due to evil reasons. You can be sure that when Apple is developing their devices they constantly look for "product differentiation", i.e. ways to differentiate their products, often artificially, to create a demand that they instead complement each other - i.e. their way trying to make you buy all their devices.
So, in the calculator case, the public explanation they gave was that "we will only include one if we can make it stand out on the iPad". Anyone with a brain would ask "just give a simple calculator one to start with... feel free to make it better at any time". The underlying reason could be that they simply want you own an iPhone and use the calculator app there.
This pattern is evident everywhere, especially with the iPad, since it's something between a phone and a computer. How can they artifically limit these devices in terms of hardware, functionality, features, eco-system, so that you feel forced to own all 3 of them for the "best experience", at the cost of your wallet.
