Because the apps can initiate a call by just pointing a webview at tel:0000.
Another reason is hybrid apps, imagine a contact hybrid app running in something like PhoneGap. You want to click a button and call right away without the phone asking you to confirm your action.
I'm not saying that Apple's design is good, but it is documented.
That was my thought as well. I'm sure the decision was made to connect as seamlessly as possible, without the user having to stop and click a dial confirmation.
I'm not saying that Apple's design is good, but it is documented.